Welcome to the abyss

The answer is simple.

CAVE. JOHNSON.

Every universe that the combine has taken over is a universe where Cave Johnson died and aperture science faded into obscurity, because any universe where Cave Johnson is alive and/or aperture science wins against black mesa is a universe where the combine lose.

Firstly, Cave Johnson is smart enough to avoid causing a resonance cascade and will cancel any test that even has a chance of causing one. We know this because of blaberture mesa, where Cave cancels a test that could cause a resonance cascade, avoiding the entire black mesa incident and preventing the combine from even entering the universe in the first place.

Secondly, 99% of the things made by aperture science are weapons that could destroy armies if they are so much as looked at wrong WHEN APERTURE SCIENCE IS PRETTY MUCH BANKRUPT, any universe where aperture science has funding is a universe that outguns the entire combine without even trying.

So the combine only invade universes where Cave Johnson is dead and Aperture Science is destroyed by outside forces.

Any universe where Cave Johnson is fine is a universe that the combine cannot enter because they definitely don’t want to give that maniac any knowledge about the combine or their multiversal empire because he will either destroy them instantly or create an even stronger empire focused on science, and since this is Cave motherfucking Johnson we’re talking about, that science will be the most unethical science you’ve ever seen, and the combine will most likely end up as test subjects.

In no particular order:

He has a stated fear of public bathrooms, in hit and run he goes behind a screen to put on a bungee jumping harness and helmet, he had a voice coach and a therapist, he describes his family reunions as awkward, says he feels jealous of other men's stronger jaw bones, he scolds Max for asking if Bosco was transformed into a girl cow, he's apparently incredibly sweaty with a strong smell, and his clones were described as "Zaftig" which is another way of saying voluptuous or womanly, which Sam didn't like. Also went to stewardess school???

Anyways. To me, this indicates that Sam is taking testosterone, as that causes excess sweating and new smells as second puberty occurs. But I don't think he's very consistent with it, he doesn't get the same results from exercise and his diet as Max does, and while it could just be max is max (and supposedly uses protein powder) low testosterone can cause weight gain and reduce muscle.