I had trouble trying to reproduce this. I picked a source to make 3 proxy test files with Handbrake using the same preset you mentioned but for some reason the 540p proxy files came back with variable frame rates. That means that every time I tried to open them in Shotcut I would get the message telling me I should make intermediate files because of the variable frame rates. So this did not crash on me. Plus, I don’t have QSV. I have NVEnc so I don’t know if the type of hardware acceleration makes a difference. I tried both the regular H.264 and the NVEnc and both gave me the same variable frame rate result.
I’m on Windows. I don’t know if that’s the same OS you are using and if that would also make a difference.
However, if you are looking to use proxies, have you seen @KKnBB’s great proxy tool? If you haven’t, check out his thread here and try it out. See if that serves you any better. 