www.makemkv.com

Is there a setting in MakeMKV somewhere for the minimum duration threshold of a 'SKIP' chapter that I can increase?

What I mean by 'SKIP' chapter is the very last chapter in the file that allows you to skip to the very end (IE skip to the next file). It's usually very short, something like a few hundred milliseconds.

At the moment these skip chapters seem to be automatically removed if they're less than about 500ms but I've been finding a lot of files lately where the skip chapter isn't removed because it's slightly longer, say up to a second or so in duration.

This means I have to open every ripped file affected in MKVmerge, edit the chapters by hand, then re-mux the file. This can become quite tedious when you have to do every episode of a TV series!

Alternately, could we have the ability to de-select individual chapters when setting-up a disc/file for ripping by having a checkbox next to each?

I would also like an option to select individual chapters.
So far, I'm ripping with makemkv then separated each chapters I want (or don't) with mkvtoolnix, then re-merge the different parts I want together (ie: removing opening/ending from TV series ... which can be quite long for a 20min anime episodes).
Obviously very tedious, so I would like for it to be selectable directly from makemkv if possible.

That's not exactly what I had in mind. I didn't want to affect the video/audio tracks in any way, I just wanted to remove the last chapter "entry" and adjust the timecodes of the penultimate chapter accordingly, not actually remove the last chapter of the movie itself.

As an alternative (for my purposes anyway), it would be enough to be able to set the MKV Flag for an individual chapter to "Hidden".

I know this option exists in MKVmerge when creating/editing chapters so there must be provision for it in the Matroska standards, but there's nothing in the drop-down box for any chapters which would allow me to set this "Hidden" flag.

I had indeed misinterpreted your "could we have the ability to de-select individual chapters", for something more global than just hidding chapters.
My bad