Yeah, same process here, just using the quickBMS and the same script to unpack the mrgs. For reference, here's my Mio:
Actually, thinking about it more now that I'm slightly caffeinated, I realized there's a large and small version of the sprites but the images share the same file name. So I'm assuming what's happening when you just export the images straight into the same folder is that one (the smaller one) just overwrites the larger file and there might actually not really be a difference between the two options besides the fact that the option that worked for me creates a uniquely named folder for each file, so the overwrite doesn't happen, also that explains why I had like a million and one filename collisions when I tried to put all those images into one folder.
Anyway, that's just me rambling. So guess first thing I want to ask is when you unpacked the BNTX it should have given you a warning about duplicate files, did you select the option to keep dupes? If so, you should have files named something like MIO_A_30_01_N01 and MIO_A_30_01_N01_00000001 (the _00000001 being the suffix added by quickBMS for the dupe). The first of those should be the larger one.