I'm not sure you fully understand how TU5 customs work. You NEED the entire RB1 midi file for verification and that's why we use the upgrade work around in the first place. I've explained it once before here
I tried using imsosick.mid from the RB1 export as the main midi file. The tempo track name for it is 'imsosick' so I renamed the tempo track name of the upgrade midi (custom song) to that. The upgrade method is used to replace/add tracks in the main midi file. But as you said, it won't replace the tempo track. What I just did confirms that even when the tempo tracks share the same name, the game won't replace the track.
Although another possibility could be that the game is only ignoring the 0th track, which is the tempo track according to standards, in which case it might be possible to replace said track if it was placed in a different position such as the 1st track. Or you could try deleting the tempo track of the upgrade midi and all the tracks that should be added/replaced should still work fine. If the new 0th track doesn't work then you'll know for sure that the game is ignoring just that track.
EDIT: Copying the tempo track to 1st position didn't work either. Oh well. It was worth a shot.