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You could also try converting the mkv to mp4 using ffmpeg and manually copy the HDR metadata over, which Premiere Pro then understands. It's just a bunch of tags telling the software what the pixel numbers mean. This can be done with reencoding, or maybe without if the mkv contains a video stream already in the right format and just needs to be moved into a mp4 (might not even require manually specifying metadata, maybe the converter you used just didn't support it). I'm not sure about formats like HDR10+ that have multiple metadata updates in a single video, you could use this to extract the metadata but I don't know how to pass that into ffmpeg again.
If the cutting operations are simple, you might have success with ffmpeg. It can be used to cut and merge video files and understands all the metadata and pixel formats required for HDR video. If you just want to extract a clip, it'll work fine, but if you want to do more complex operations, things could get messy. I'm pretty sure there's some setup of convoluted commands and pipes that could get that working without generating gigantic intermediate files or losing some quality by reencoding repeatedly, but that seems like an unreasonable hassle (video editors conveniently automate this).