I'm not sure where to begin looking for what I'm looking for (if that makes any sense, haha). I didn't notice anything that suggests there's a table/list of how long each file is supposed to be. From a programming standpoint I thought that each time the game has the instruction to play a certain file, it also gets an instruction to pause (ie [trigger happens], play MXX.PCM, wait 28 seconds, play MXX.PCM, wait 2 seconds, etc). I burned another copy with M62.PCM being shorter than it should be and seeing if it gave a delay before loading M63.PCM, and it did not. Instead, it immediately loaded M63.PCM, which leads me to think it doesn't have a "wait" instruction and has something in place to keep track of when a file has finished playing. This is definitely perplexing, and really begs the question of why it can't play the longer files if shorter ones perform seamlessly.
I went a step further and burned a copy where all I did was swap M62 and M63 to see if the game would still proceed past the opening (since they'd add up to the same length and they're GA's original files). No dice. Perhaps it's something like when it loads a PCM file it also pre-allocates a certain amount of memory for it, so if the file is shorter it's fine because it has more than enough memory, but the other way around, it'll cut off at the point the memory allocation runs out.
The PSX version of the game seems like all the audios are grouped together, so the way it plays them might be different. Like the Playstation might be something like:
[trigger happens]
play LUNAR_DA.PCM from X:XX:XXX to Y:YY:YYY
do next thing
This is totally an assumption of mine, though I'm sure that's obvious xD
Another oddity is that M01.PCM-M61.PCM are in both the root directory and the battle files directory on the Saturn disc (though it's possible they simply didn't clean up all the redundancies when they published it).