Using an IFR flight plan with ATC in MSFS 2024 can absolutely disrupt your FMS flight plan. For example, I've had certain waypoints entered, and when ATC assigned an approach and arrival to me, it automatically swapped my FMS waypoints with their assigned ones (which caused issues). At this point of my testing with Starship 1.1 I believe if you want simple ATC, you simply select the departing and arriving airport in a minimal VFR plan and start a flight with that. I also plan to do a few more flights by starting with a simple EFB-created IFR flight plan with only departure/arrival airport, request IFR clearance and see if I can preserve my flight plan all the way. I use the Simbrief EFB app to create my flight plan, but copy/paste all values manually into the aircraft, never importing it. When ATC assigns an approach to you it's likely that you'll still have to fix things, but most of the flight should be fine. I hope version 1.2 will guard against such flight plan injections from ATC.