Realised by this case that it would've been worth to note that to get the sound of the render, the player should make an instant transition to the next subsong after all loops has passed (dunno which players that can do that? I haven't figured that out in xmplay).
Although all kinds of ways the players handles the transitions are correct (although crossfade is a little ugly imo if it isn't in time of the beat lol), as long as the subsongs are played in the prologue, main tune, epilogue order.