unmo3 doesn't change subsongs in anyway.
The problem is just that most module formats, including the ones that MO3 supports, do not really have a concept of subsongs. People have found clever ways of embedding more than one song into a single module file, though, for example by simply putting all songs in different patterns and putting them one after another into the pattern sequence. The user then has to figure out which subsong starts at which sequence position.
Players like XMPlay can figure out this information on their own, so if you throw an MO3 file at XMPlay, it will correctly split the song up into subsongs. However, if you decompress the MO3 file and then load the IT file into some other tracker or player which doesn't apply the same tricks as XMPlay, you will have to figure out where the subsongs are located on your own.
If you load a file with subsongs into OpenMPT and use its song length estimation feature, it will try to figure out the different subsongs pretty much the same way as XMPlay does. It will never auto-advance between different subsongs though.