Maybe look into PipeWire, Reaper in jack mode works fine connected to PipeWire for me, without any of the problems you mentioned.

It is quite possible that your desktop audio already uses PipeWire depending on your distribution, you would need to look at latency settings if you want live playback.

I recommend https://github.com/kmonad/kmonad

There are other ways to structure and edit programs than just a bunch of source files that we manually edit through a text editor. For instance image files as in Smalltalk. I don't see any reason why a visual representation couldn't succeed in this regard. The issue, imo, is that text is really nice to work with, and it would require a very nice visual editing experience to beat the text based tools we have today.