If you're changing from one Rega platter to another Rega platter, there's probably no change in alignment. You should have been provided an alignment gauge when you purchased the table, use it to check for any variation between the two platters. If the vertical tracking angle remains the same, then nothing else should change when switching platters. Set the guage on its long end against the arm when it's positioned on a disc and check for vertical alignment with one platter and then do the same for the next platter. If you don't have an alignment guage, just print out a long straight line on some heavy stock and set it against the arm. Unless you suspect your VTA is not properly set with the MDF platter, it doesn't matter whether the arm is parallel to the line, it just has to match between the two platters.

Are you using a Rega cartridge? From what I have been able to tell reading various forums, the VTA of a Rega table is correct only when using a Rega cart or one with the same dimensions.

If you are using a non-Rega cart, the tone arm will run ass-low, so to speak. Rega sell spacers of varying thickness to bring the back of the arm back up to level.

I am running an AT 440mla, and have installed a 2mm spacer to bring the arm up close to level.

Putting that aside, I am not sure my ear is such that I can hear the audibility of VTA, but since the spacer was short money, I followed the crowd.

Brian

Edit: I forgot to mention that I too swapped the MDF platter for a Rega Glass platter.