I've created a little IFR flight plan from EBOS RWY 8 to EBBR RWY 25L (in the TBM-930).
For my problem it doesn't matter where the flight plan is created, Simbrief, the MS flight planner or directly in the EFB.

I go free flight, load up the EFB, load the flight plan and then hit File plan with ATC.
The moment I do that, the start and destinations on the world map are filled in but not always correct.
Instead of EBOS RWY 8 it sometimes takes RWY 26, same for EBBR. Today it filled in RWY 19 for EBBR to land while according to Flightradar RWY 25 R and L were in use.
However, when I press "File plan with ATC" a second time, it sets the departure and arrival RWY's according to the actual flight plan.
I then start the flight and this all goes fine until I'm lined up finals for RWY 25 L.
I then send my flight plan to avionics.
I start the flight, set up autopilot and let it do it's thing, ATC switches me to on approach, directs me down to 4000ft, all goes fine until I'm lined up finals for RWY 25 L
ATC then all of sudden wants me to change to RWY 19 for landing like it did in the beginning (and directs me to a navigation point which I already past).
I can opt to request to land on 25L instead but ATC never accepts that, even when ATC confirms that I want to land at 25L, the next ATC message directs me again to RWY 19.
From there on it's a mess...
It doesn't matter if ATC enforce flight plan is set or not in assistances, it always gets messed up if the flight plan ends with landing on a RWY that doesn't correspond with what the ATC of 2024 had in mind in the first place (RWY 19 although that is wrong).

How do i deal with that and make it work better because it just destroys the entire experience.

Basic sim issue not eliminated since release of FS2004 if I am not mistaken?