www.makemkv.com

Is there a way to in MakeMKV to specify the output file names per source item so that I do not have to rename them after the export?

Do you mean besides the menus? I've always used the Properties->File name when looking at the individual titles when I want to change the file name as it is ripped, rather than after-the-fact.

Where do you see the option?

For example, in the screenshot above, I would like to change the name to be more descriptive that would work with PLEX. Many of the disks I have just get named {Disk Name}_tXX.mkv where XX is a serial number for the tracks.

Ah... Go to Properties->General, and click on "Expert Mode" to turn it on, then OK.

THEN you'll see the Properties sub-menu on the main screen. I've used Expert mode for soooooo long that I forget what it enables.