I've gone down the monolith with Backbonejs, Angular, and React. Using just Stimulus and Hotwire is a breath of fresh air. Though, to your point, it can be difficult when you run into those "edge cases" where you need something to happen that the framework doesn't have available. There is some great discussions about this on this GItHub issue https://github.com/hotwired/turbo/issues/92 as well as some potential solutions.
I've ran across some of the issues that you're describing too. Specifically, when there is something like ChosenJS that you want to have rendered from a Stimulus controller, but cannot invoke the chosen() function because of the whole jquery stuff. Some of the solutions in the link above could help address these issues, but what I've done in the past is work towards moving away from the jquery libraries in favor of something with vanilla JS. However, I can empathize with people who have heavily invested in one JS library that is used throughout their application.