Significant performance differences executing alter and grant statements between users with same permissions
TL;DR; Check database triggers
It turns our this was a very narrow, unique issue - but one that others might experience in a similar setup.
The performance issue was being caused by a database trigger that was called on grant, create, and alter statements, and based on the user, executed additional (sometimes heavy) logic.
These triggers were running extra logic for the accounts I was testing with, but not the original account.