As long as the flight plan uses published SIDs, STARs, approaches, high or low altitude airways, ATC won’t fly you into any mountains. The problem is with direct vectors by ATC. MSFS doesn’t contain the Minimum Vectoring Altitudes.
This is similar to using the Direct function in a GPS. The GPS direct vector may not provide obstacle clearance. Published IFR charts contain “off route obstruction clearance altitudes” for map quadrangles. Unfortunately, MSFS does not provide these charts. Also, MSFS does not contain ODPs, Obstacle Departure Procedures. These published directions (similar to missed approach directions) contain vital information not in the SIDs.