Let me boil down your essential claims:
1) Bacteria in the gut make stuff you need and helpfully digest things for you.
2) Endotoxin is only a problem when it crosses the gut.
3) By various magic bacteria in the gut strengthen the immune system.
Well #1 just isn't really true. There aren't any identified compounds that are at all hard to get from food that you need gut bacteria to make for you. Maybe some vitamin K and that's about it, but a serving of liver or some other foods will more than cover your vitamin K dose.
#2 is a silly argument because endotoxin is constantly crossing the gut barrier. LPS endotoxin is a continuous stress on the liver to detoxify. Whether it's a real problem in an otherwise healthy individual or not is a separate question, but the argument presented here is totally specious. It is quite plainly a continuous stream of toxic material the organs work to clear.
As for #3, that's the big totally open question I guess. You see the claim made but nobody ever really breaks it down in detail in terms the experimental physiology proving the idea. It's usually some eye-roll-worthy trials.
The fact that the sterile rats can't survive outside the lab environment is not the point. No kidding they have under-trained immune systems. The point is that absent the chronic stress of bacteria load they do in fact live longer and are in fact stronger in the literal definition of strong. This guy is being deliberately hand-wavy.