Last night I tried a few of these things out, with some limited success.

Sorry in advance for the long post!
First of all, what a great suggestion it was to heat the carrier/rotor shaft with a hair dryer. For anyone looking to remove this part on your Mazzer, I highly recommend this method! It made the removal process much easier. The 3-screw method now required much less force, and after just a few turns the carrier slid right out.
Once I had everything removed, I was able to compare the carrier-less shaft with pics from this thread...
Help with Mazzer Super Jolly Disassembly, and mine looked strikingly similar. Notice the shoulder is indeed sitting well above the sheet metal bearing cover.
After another thorough cleaning, I gently positioned the carrier back on the shaft, again minding the pin, and shined a flashlight into the chute as i heated everything back up with the hair dryer. Again, it was so easy after heating that I could seat the carrier entirely with my bare hands. Looking through the chute, I was sure the positioning was spot on (in fact, I tried it once intentionally missing the roll pin so I could see the difference...it's a very obvious one, btw), and I was able to hear an audible "click" as it came to rest on the shoulder. I then replaced the center bolt, and was certain this thing was now properly seated.
JohnB. wrote:Another option would be to slip a piece of pipe over the shaft and tap on that so you would be hitting the flat burr carrier instead of the shaft. Since the burr carrier sits on a roll pin in the rotor shaft this would reseat the shaft to the correct position if it has indeed moved up without risking damage to the shaft.
Before reassembling everything, I wanted to try this, so I placed a 3/4" x 2 1/4" rubber washer on the carrier, and using a small block of oak on top of a 2" piece of steel pipe, I gave it a couple solid hits with my hammer. I had the bottom cover removed so I could see if anything was moving that otherwise shouldn't be, and all seemed fine. However, this really didn't seem to be doing much. Not wanting to overdo it, I stopped and put everything back together to test the grinder.
The zero point is now about 7 notches lower, so evidently the re-seating/tapping combo did help a bit. The collar still isn't quite where it was before, and could come around another 150 degrees or so. Nevertheless, the grinder does seem to be working fine, so I just may leave it. Unless of course anyone else has other suggestions
-Mike