We don't need the bodies to function. We need them as an organ growing environment. The muscles will atrophy, so what.

Then you cannot use the muscles, and you've just lost one the of the initial use-cases. Repeat it for any organ that need a functional body for its development and you might end up with really few useful parts from your “factory” actually.

Few is better than none, and at least for muscles, you could simulate the "stresses of everyday life" with machines.

All I see are bioengineering problems. Once we start hill-climbing this solution path all the problems will become shallower and shallower.

You can't use the animal muscles as well. What organs need moving, active body, if you can control hormone levels etc?

Well, then, can you mechanically create those stresses? Regularly send electrical signals to exercise the muscles, increase and reduce pressure and temperature (even have robot-controlled plates do a full massage), stretch and vibrate the whole setup, cycle through levels of certain hormones...? It may take some experimentation, but once you figure out a process that works, you can grow millions of organs with it.

(The story "Mazer in Prison" mentioned, offhand, someone getting his muscles electrically stimulated while he slept as a substitute for exercise.)