I originally had started out with all the plugins compiled into one package, but that is a bit much if someone just wants to just upgrade VapourSynth. I understand it can be a pain to download all the plugins individually, however unless I find a better way to host them it is just how it has to be for now.
The installer was made with the software
Packages, my recommendation to make it easier for others to use Hybrid would be to create a companion installer that has the dependencies and places them where they need to go. If you want I am more than happy to help you get started and answer any questions. I'm involved in a lot of different things and I just don't have the capacity to cater to every software that has certain dependancies, I actually haven't had enough time to keep up to date with all the plugins since no one else is contributing at this time.
As for upgrading stuff, I would not recommend replacing system files at all, I would replace things either in the app itself or self contain them like I did with the VapourSynth installer and create link files if needed. Dependency locations for dylib files can actually be changed, if you need any help with this feel free to contact me as I know it can get a bit complicated trying to avoid replacing anything on the system level.