You should have no problem transferring to the new console and not have to rewire and readdress your fixtures. The extra universes are in case you need them, meaning more then 512 channels of lighting, or can make your life easier at times. For example, if you have lights at one side of the room and lights on the total opposite, instead of looping them all together, run one DMX line to one side and another to the opposite side to save on cable and stop possible issues that may arise.
As for fixture profiles being 32 channels of DMX, that isn't the case with the SD3. It can control 48 fixtures up to 32 channels a piece. Even if it was the case, you can re address the fixtures so they over lap and just not use the extra channels. I have that problem with a Magic 260 and Trackspots. Trackspots are 7 channel fixtures, and the Magic 260 has generic for 8 channel. Since the Trackspots use there own DMX dip switch settings and not binary, I am forced to use them as 7 channel fixtures. So I simply make fixture 1 channel one, fixture 2 channel 8, fixture 3 channel 15, etc. Even though the 8 channel fixture profiles should be fixture 1 channel 1, fixture 2 channel 9, fixture 3 channel 17, etc. I simply don't use the last channel on each fixture.