I've had the turbos on a Ford 6.0L apart a few times and it is harder to get them off of the engine than it is to separate the exhaust housing. Scrubbed the vanes and unison ring with a scouring pad and some parts cleaner. It really is an easy process (at least it was on the 6.0L stock turbo), and wouldn't hesitate on yours.
In my opinion there is no reason to pull one apart unless you are experiencing sticking issues (overboost/overspeed, or underboost) and could even be causing the engine to defuel.
As for tolerances, you must be extremely negligent to get something out of line (drop the turbo while it is apart and bend the compressor or exhaust wheel or even bend the shaft), break one of the wheels and cause an unbalance, ect. The compressor (intake) side stays together, you are opening up just the exhaust side for cleaning.
