keyman VS PIPIT

Keyman is very popular among linguists, if you still prefer a keeb that will input IPA Unicode by itself, you can get a QMK compatible keyboard (like this), but you'll need to program it, as in write the code yourself.

SIL's Ukelele is a popular app for creating custom keyboard layouts on macOS. SIL also recommends Keyman if you're looking for a cross-platform app for creating custom keyboards. Keyman already supports thousands of languages so they might already have a keyboard for the languages you need.

While I haven't used it myself, I have heard that Keyman is highly flexible and extensible, so it may allow OP to create a layout in its own format that has the desired behavior. Keyman was originally a commercial product, but SIL (which had long advocated its use) acquired it in 2015 and made it free shortly thereafter. The original developer seems to still be part of the team working on it for SIL.

They aare on github here: https://github.com/keymanapp/keyman

For Tam Thư, specifically the phonetic Latin Quốc Ngữ and Ký Âm, I'm working off of an existing keyboard distribution platform called Keyman. It's free and open source with good developer's guide. For my case, Vietnamese typing is a bit complicated with many key sequences that makes modifications to a base glyph, and Keyman is a fit tool for that in my experience. It also follow the principle of "write once, run everywhere" since your compiled Keyman keyboard will run on Windows, MacOS and Linux.

From your description, yes, it sounds like your concerns revolve around deficiencies in existing keyboard layouts and possibly fonts, whereas Unicode is not concerned with those things (it has an influence on them, but is not a standard about font design or input methods). You could potentially mitigate the keyboard issue by creating your own custom layout with something like Keyman. The font part is harder because making fonts is...well, hard — but you might check out some open source font projects that support Coptic (like the Noto project), file an issue, and maybe let folks know of your willingness to provide guidance and advice even if you're unable to do the actual font work.

If you don't know what keyman is you can check out their site here https://keyman.com

You could try using the software I'm using. I tried the Windows 10 keyboard and I didn't like it. Seems it was designed more for Hindi than Sanskrit. I use Keyman which you can find and download here for free: https://keyman.com/

GitHub: https://github.com/khanming/Pipit