There are no differences with the endings, but that is not the case with all OMV videos. For example, in Hatsuyuki Sakura they use OMVs to show the date. This is what it looks like in the game:
And this is what the player shows when extracted:
It seems that someone did research this file format and that my theory was correct:
There are two types of OMV video files, 24-bit and 32-bit. 32-bit OMV files incorporate a specially-encoded alpha channel (to record transparency), and thus cannot be correctly played by most video players and editors.
https://github.com/xmoeproject/SiglusExtract
Unfortunately, they didn’t include tools to repack these files. But at least now we know how to read them.
Also, that tool lets you modify the name of the “scene.pck” and “gameexe.dat” files.