The .mptm format allows for multiple subsongs/sequences in one module file, which I am using in order to have my game read the whole OST from one compact file. I am interested in using .mo3 to reduce filesize even more.
I found that the mo3 encoder will automatically try to detect unused samples to remove them, but fails to detect the usage of samples in sequences other than the first one, and these samples end up absent in the output. There doesn't seem to be a way to counteract this with the console encoder; the GUI encoder does allow re-enabling the samples again, one by one, which is tedious to do as there's over a hundred (possibly more in the future).