I've also been tinkering with these files for a while, and I think I've finally cracked it.
The attached script should extract both the .at3 and .vag files from the .sep archives. It works on every .sep file, so there shouldn't be anything missing.
Hi sorry for the late reply. I ran the script on most of the sep files and it is definitely collecting a few files in the "se" labeled sep files that the original script could not. Foobar couldn't run them, but off the top of my head I know PSound runs .vag files so that let me have a listen. One of those files gotten with the new script is one of the missing voice files that I'm looking for, because the game devs mistakenly threw a couple voice lines in the sound effects file container for that scene
I'm still on the hunt for a lot of material. https://youtu.be/2GHmjrapWoE
This video is a representation of what I do have, not counting a few additions I've picked up on later passes. I think the biggest issue is I just don't know where it could be. Some scenes have no corresponding sep files, while others that should have what I need are blank in terms of code. The Oss folder seems to be the only place in game data where they keep cutscene audio, so I'm stumped.
Everything extracted from the sep files with my script plays fine in Foobar, and I can't see anything missing. More cutscene dialogue is in the .pmf video files in the mpg folder, which is where most of your missing audio seems to be. The dialogue there is mixed in with the music, but you can extract them with VGMToolbox. For example, the first missing lines from your Youtube video is in the file "s04_06.pmf" ("You heal up pretty quick", etc.)
After some further investigation, there are also some short voice sounds in the stage folders, specifically the "_zar" files in each folder, which are zlib-compressed. If I work out the format, it should be possible to extract those too.