I know this wont help with existing installs but moving forward isn't there a way we can do something in core to include the package id with discovered installs.

The same thing happens with languages

That was my original idea but, unfortunately, you can't :( You'd need to a. be able to use Discover for packages, b. guarantee that packages are installed before other extensions and c. figure out how to handle orphan extensions based on packages installed during this Discover session or previously installed.

a. You can't discover packages. They are just a manifest which tells Joomla to install other extension archives. Trying to install them would fail. You'd need a special case to just copy manifests and create missing extension records which is gnarly.

b. This runs counter to how Discover works. Yeah, it can kinda sorta be shoehorned into the existing installer architecture but I'm afraid this would cause more trouble that it'd solve.

c. This requires some serious refactoring of the installer. Considering that all previous white papers I've written were met with something along the lines of "great, but there are not enough people who understand the installer to do maintain it" and combined with the fact that most people who did understand the installer have already left the project I don't see this happening anytime soon. It'd require an influx in quality contributors, interested in how Joomla works at the lowest level and who understand its architecture thoroughly.

Not to put too fine a point on it, I think that changing com_joomlaupdate, already transformed into a Frankenstein's monster compared to its original scope, would probably be much easier. If something breaks there the user can override the false information displayed and proceed with the update while someone monkey-patches it. If something breaks in the extensions installer Joomla is dead in the water.