Engineering is done in the context of constraints, cost is one constraint - and its a relatively conserved constraint. Saving labor in one area allows for more care in other areas. Especially given that labor is often not cost constrained, but skill constrained, which is less elastic.
NASA is an organization that is dysfunctional and way too expensive for what it does. It then decided to use agressive cost cutting to cover up these problems.
The fix for not doing that by hand is to get a robot to do it, given the applicator is human-held, a human-strength Kuka with enough reach to cover the area it can handle before the applicator needs refurbishment of some sort which would give a good opportunity to move the robot to a new section of the heat shield.
So cost cutting, as always.