I don’t think you’d need to do anything particularly special to get that working. The Cinder-WMF block does a good job with hardware accelerated video playback (i’m assuming you’re on windows) but I don’t think it supports alpha channels and the last time I used it it had some problems with playing back multiple videos at once, but that may have been addressed in the interim.
If it were me I’d probably use HPV for this since your videos are quite short. It supports alpha and lots of simultaneous videos as well as synchronous seeking which will be good for if you need to be frame accurate across multiple videos (i.e the layering you mentioned) at the cost of some larger files and a bit more disk thrashing. I recommend a decent SSD for it.
I’ve used HPV in the past in some decently exotic setups and it’s held up well. Unfortunately I’m not able to release the production code but i posted an early precursor to it here that should give you something to play with. There’s a ton of other relevant info in that thread as well.
For the control stuff i’d just use OSC or TUIO, but there’s 100s of ways to skin that particular cat and none of them are particularly taxing so you should be fine with whatever method you go with.