Concern #1:
In most cases it's possible to trace the "An Audio Unit plug-in reported a problem (...)" error with console.
Utilities > Console > crash reports
I had many of these issues with a few plugins even they were all up-to-date. After updating my macos from sonoma 14.7.3 to Sequoia 15.3.1. (now 15.3.2) the issues disappeared.
Concern #2:
Yes, the time stretch algorithms are out-dated but there are nine different time stretch algorithms available when using Time and Pitch Machine in the Audio File Editor and six algorithms in Flex Time. Did you try them?
Concern #3:
There are some Midi-FX-plugins like Modulator, Modifier and others that are worth to look into it. Also check the Scripter Plugin.
Concern #4:
Yes, I agree, the view is out-dated and not exact.
Concern #5:
I second EddieGrey’s suggestions and like to add, you could assign a third quick tool to some windows by selecting Settings > General > Editing > Right Mouse Button > Is Assignable to a Tool
BTW: It's always a good idea to provide information about your Logic version, MacOS and Computer Model.