Or just another way of looking at it. The beauty of the Skrull milk explanation is that it does not contradict other explanations. It merely fills in the gaps. That is, whenever another theory has hand-waving "that is comic book science, move on" the milk theory provides the details. 

To illustrate, how do cosmic rays fit in if Reed's stretching is just being a shape changing Skrull? I  imagine a scenario like this:

1. Aliens exist
   Skrulls exist in a far off galaxy. But otherwise the MU is the real world as we know it. I think I can make a good argument that Skrulls must exist out there somewhere (a variant on the SETI argument) but that's a different topic.
2. An alien escapes
   On a visit to Earth, one Skrull escapes. We'll call him Reed. Skrulls generally hate being Skrulls (see FF 2) as most are just hypnotized to be cannon fodder. 
3. He know they will come back for him
   He has t So what does he so? He manages to grab as much tech as he can from the saucer without being noticed. Maybe the other Skrull thinks he got killed, so thinks nothing of it. (Life is cheap to Skrulls.) But sooner or later Reed knows they will return to destroy him and possibly the Earth as well. How does he prepare?
4. He tries to build an army
   His only assets are the ability to change shape, and to breed other Skrulls (using Skrull milk). Plus knowledge of Skrull tech. So he could "Skrullify" people and animals to form an army. Plus Skrulls are easy to hypnotize, so they would not know they were Skrulls. I think Reed created at least three armies in hidden places, and gave them fake histories, so they thought they were very ancient. But there is actually no evidence for them before the 1930s when Reed appeared. He hid these armies underground, under water, and in remote mountains. We know them as Monster Island monsters, Atlanteans and Inhumans.
5. It does not work
   But the down side is that easily hypnotized groups can be controlled by others as well. So he soon lost control of these armies and they developed their own "us versus outsiders" cultures and mythologies. So what can he do?
6. He tries to create handpicked heroes
   So he focuses on studying Skrull biology (we know it as unstable molecules) and the most valuable Skrull technology: not just the flaming suit and transistorised stuff, but the jewel in the crown: faster than light travel. That is based on dimensional warping, and Reed can imagine a lot of other uses for that. He spends the rest of his life studying that, in an effort to create a kind of Skrull-human with the right balance of intelligence, heroism (caring for others) and particular power sets. Over the years he empowers superheroes. 
7. The technology spreads
   Reed's science naturally spreads. The number and sophistication of superheroes grows. An arms race naturally develops, where every advance is copied and built upon. So mch is at stake that the brightest minds on Earth (and beyond where possible) are constantly improving what is possible. To illustrate the range of these superheroes, the first three are:
8. Namor
   One Atlantean had greater intelligence and abilities and took control of the first and biggest army.
9. The Human Torch
   One man was given the Skrull flame suit (standard issue on  Skrull saucers: see FF 2), and a Skrull's ability to survive wearing it. Reed (calling himself professor Horton) did not get it quite right, it tended to turn on in contact with air. But Skrulls also have the ability to go into harmless suspended animation when buried (see the super skrull in FF 19; the Dragon man shows a similar feature). So Horton (Reed) just said "it's not alive, it's an android" and buried it in concrete. Skrulls think nothing of that as they can wake, shrink and escape whenever.
10. Captain America:
    The super soldier serum is Reed's attempt to share a very precise mix of Skrull Milk with the government. He later lost the exact formula.
11. Cosmic rays
    The holy grail of course was to use technology to improve Skrull abilities beyond what the Skrulls themselves had. This is where the cosmic rays came in. Reed could have just given his friends milk and hypnotism - "you can shrink and therefore appear invisible, you be a monster, you wear the flame suit, and I can stretch already." But he tried to make them stronger. After thirty years of research he feels ready to intelligently mutate the DNA even further. Give them something more. BTW I strongly suspect that in later years, every time Reed "studied" Sue's invisibility, or tried to "cure" ben he was also finding ways to increase their power. Because that's what happened as a result each time.

"But... but..."
Note that none of this contradicts the main established facts. For example we are told that Namor was the hybrid offspring of Leonard McKenzie and Princess Fen. In my theory he was: Reed (calling himself McKenzie) would have fallen in love with some girl and given her Skrull milk and hypnotism to let her live underwater. He then had the idea of increasing the potential for beneficial mutation by perhaps sleeping with her (Skrulls have a different concept of morality, and besides, the fate of the world was at stake). The offspring was Namor, and since Skrulls are shape changers he could be an adult the day he was born. The only apparent contradiction is in the dates: to avoid drawing attention to himself Reed would give people new identities and fake histories. Everything described in the comics actually happened, but in the 1930s, not over thousands of years. Comic fans are used to sliding and telescoping timescales, so what's the problem?

Minor details are changed to protect the innocent.
Also, since Reed (and others) rely on secrecy, and all we know is Marvel Comics' reporting based on Reed's monthly meetings, we cannot be sure every detail is correct. But Marvel does its best. For example, Peter Parker kept his real identity secret, so Marvel comics changes those details to protect the innocent. And when Aunt May brings Peter his glass of milk, we are not told where that milk comes from...

tl;dr the theory changes nothing, except minor details to protect the innocent. It just gives the background to what we already know. 

In the words of Han Solo, "It's true. All of it."

According to the Marvel Wikia entry, the Celestials also created the Skrulls. It looks like they did their business everywhere.

Obviously, entities of such power can make you think whatever they want, that's a given.

Inspired by the better than expected response to this thread, I turned it into a permanent page, with a snazzy title graphic.

zak-site.com/Great-American-Novel/ff_milk.html

I also found what may be the first example of Skrull-Reed (in disguise, naturally) experimenting with Skrull milk. Here we have Uncle Ben (younger and slimmer) and Aunt May (also younger) giving milk to a girl who then becomes a mermaid.

I think she was from the 1930s, and this is a dry run for "Leonard McKenzie" and Fen. And it went so well that Ben and May were chosen for another, even more successful experiment later. Of course, their memories may say different, but see how everyone sleep walks: clearly there is some heavy grade hypnotism going on. 

No doubt. I am sure that a typical Skrull has a hundred different identities and can turn up anywhere he wants. THe only question is whether Skrulls can have multiple personality disorder, so each identity is unaware of the other ones.