Drums sound different and vocals seem to be more quiet in later recording.
A nice gentle tune with such sweet vocals. 
If the drums have been changed, then it is a new recording.
If the vocals are quieter, then that is just mastering, and therefore the same recording.
I can’t see those vocals being easy to reproduce exactly each time.
I may give the two tracks a few listens so will edit this post shortly… if in doubt best to leave as two separate recordings and maybe leave some notes in the recording annotation as to your thoughts.
A test I often attempt to do is play both tracks at the same time. Not sure how well that could work here. Too much going on .
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Am trying to listen to this swapping back and forth a few bars at a time. It is so beautifully complex that it is hard to tell, but it does sound pretty similar to me. I can see why you think they are the same recording.
The more I listen, the more I think it is the same recording.
Can you give time stamps of where you think the differences are?
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I didn’t find any at first, but I think the silence in the middle of the song has different lengths.
On later recording it’s after 1:16:25 while on original it’s after 01:36.
Other than that, the only differences I hear are the drums overall. Like it’s played on different drum kits.
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If you feel it is different kits, then keep them apart. I’ve now been distracted into their Bandcamp page… so not listened enough to spot the finer details.
I tried listening to a few bars of one, pause, listen to few bars of the other, swap, repeat. Felt pretty similar but I’d need to listen to more.
If a remaster has added a new drum track then it is a separate recording. If someone has just messed with the levels a bit then it is the same recording.
Now bar to annoying the neighbours with more volume
About different kits, it’s hard to say.
The artist (UNDEAD CORPORATION) has a drummer credited pretty much only on their studio albums.
As for Touhou arrangements which this track comes from, usually Pine Tree is mentioned for arrangement, guitar, bass, programming and sometimes someone else for lead guitar.
More quiet? 
If you think they are different, then just leave them separate.
Are these the two recordings in question?
- Original MB recording: AcoustID 052a4329-d53a-493f-97cf-832a24aaeaa9
- Later MB recording: AcoustID a08c4297-0bb4-456a-8aae-bdf3b6bfccac
Those two AcoustID don’t completely overlap.
Beautiful calm lullaby. Ideal to send baby to sleep.
Quiet in a track list this stands out. Need to take a breath at some point
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I gave it a quick listen and it’s clearly a different mix. The drums are more up front in the mix in the compilation video (especially the tom-tom) while the drums are more buried (less audible) in the mix in the second video.
One difference I notice - 20 seconds in to https://www.youtube.com/watch?v=uuqKY3t4LHQ - at the second bar of the scream, there’s a distinctive series of nine 16th-note cymbal strikes panned right that are completely missing from the https://youtu.be/2PGBZC7DFE8?t=4512 version, and the snare pattern that switches up at that bar is also a lot louder.
Another distinctive clangy cymbal hit shows up at 1:31 in https://www.youtube.com/watch?v=uuqKY3t4LHQ which isn’t at 1:16:22 in the other.
Again at 2:15/1:17:08, 16th note cymbals are missing, or mixed so quietly I’m not hearing them.
The vocals sound pretty much the same to me, besides the recording having less high frequency sounds overall in the https://www.youtube.com/watch?v=2PGBZC7DFE8&t=4492 version.
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I can hear the cymbal in both versions, though in later one it’s less audible probably because of loud snare drum.
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I can hear cymbal in both recordings again, though there are a multiple of them so I’m not sure if those are what you mean. They are followed up by 3 or 4 snare drum hits and that good sounding snare drum hit (idk the proper terms for explaining it).
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I can hear cymbals here as well, but as you say, they are very quiet.
I think there is a bit of echo on the later recording after the first scream.
I guess that would seal it as a separate recording.
I haven’t listened to the tracks in question yet, but most everything that’s been mentioned seems to be mixing differences, which means a seperate recording
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