Well, the SRT files don’t shift positions, and the English subtitles don’t shift positions either, so Im not sure that would help. I do my testing with German SUP files.
If you’re running an architecture that supports Wine, I believe you can run TSMuxerGUI in Wine to create an M2TS file that can then be played by VLC. I think there might even be a Linux native version of tsmuxer, but I’m not sure if there’s a GUI.
I am watching for just “flow” issues overall (just watch the movie and see how it feels), and both of the cases where I’m considering reverting back down are very borderline – I could see a reasonable argument either way. It probably wouldn’t take much to convince me to leave them at the top. The difference is that all of the others are clearly better on top, so no argument needs to be made.