@[Ariel] – thank you for pointing this out. Of course using app.saveFindChangeQuery() is the answer for one part of your problems.
The other one about using the app.findTextPreferences (or anything around that) without afftecting the UI, I have no positive answer. It's tied directly to the UI. Unfortunately to the app and not to the document class (that would be the workaround).
Thinking out of that box: If there are two different InDesign installations available, you could swap the task to the other InDesign app, coming back to your original later. An "esoteric" solution…
Uwe