Thank you for all the comments.
I realized lying in bed last night the main problem I have (that I didn't mention above) is that my amp cannot play the EAC3 audio - so I cannot get 5.1 without tweaking the file. My editor does that, but it kills the embedded subtitle files within the .mp4. Some of the videos do need subs.
Further, I am used to chapters. I tweak all my shows etc by adding chapters after the title sequence / previously on segments so that I don't have to watch them again and again. Bang...push the chapter button and you jump over it. Without chapters in the .mp4, you can't do that. Kodi only seeks a specific timeframe step. Makes the whole process of finding the exact point quite tedious. MP4 does do chapters supposedly, but the tools I have to create chapters only works with other formats (namely DVD & BD >> MKV). I also like to remove credits / logos, which saves a huge amount of space on the HDD's. I guess I also only want a single file to deal with.
These are all the things I have been used to. I'm an oldie, so dealing with change is difficult, and the brain no longer works like it once did. Learning is slow
Yes...the MP4's play on my HTPC as is. I'd like a new amp, but funds are scarce. Tweaking the file is the only way I get 5.1 in the current setup. MKVToolNIx does NOT show the embedded subtitle files.
I figured perhaps someone here had a way of dealing with these things when starting with a MP4. I've never had to deal with MP4's before, so I was hopeful.
Many thanks.