I love my ultrasonic cleaner!
Castrol SuperClean (or Purple Power, same thing) is far and away the best "non-toxic" paint stripper I've used. Be sure to wear gloves! It will strip the oils from your skin in seconds. I soak overnight (or longer as needed) and then run through the ultrasonic in plain water to loosen the really deep nooks & crannies. Then I scrub the remnants off in the sink with running water and a toothbrush.
The concern about isopropyl alcohol is it has a lower flash point and an ultrasonic cleaner generates heat, even without the tank heater on. I haven't been willing to test it in mine as I don't have a spare flash hood just in case it does ignite. I hadn't heard the baggie idea before, but that might work assuming it's a quality bag. The baggie would have to be in the tank full of water to transduce the sound waves. The only reason I can see to even try IPA in an ultrasonic is to clean 3D resin prints before curing. The potential dangers of flash fires and aerosolizing IPA outweigh my curiosity as to it's effectiveness.
But the point of the ultrasonic is to use sound waves to shake loose dirt and residue. The medium just has to be liquid, so water is the safest, easiest, and cheapest option to use. A couple of drops of dish soap helps if you're cleaning greasy parts like from a gun, but that shouldn't apply to models being stripped.