No the panels dont have to be in bare metal to apply the epoxy over.. We suggest bare metal however so you know what you are starting with from scratch.. The job is only as good as the foundation, just like your home and you may spend thousands of dollars on materials.. so its cheap insurance to strip to bare metal..
Doesnt take that long and you know exactly what is there..
For example.. Not too long ago I took in a car for a repaint.. Only had one paint job on it.. Was stripped 15 years ago and was a garage queen.. Ended up with panels needing replacement etc.. So when I started stripping adjacent panels to those i had replaced, what did I find....... Rust... Would not have found that, if I trusted the other paint job..
So let me put it like this.. Epoxy is the best thing you can put over a substrate of any kind to build off of.. It is however best when used over bare metal to ensure the best possible end result!!!
As for the underside.. strip what you want here again and seal it all with epoxy... Make sure the underside is de greased and washed,.,. and all areas you want ot epoxy scuffed..
Same rule applys here as well,, You dont have to strip it, but it would be best to konw what you are starting with
Hope that answers your question