Here is a age old problem area for the following reasons; Parts mgr is most likely on a program and needs margin on the sale, The service tech wants the job done ASAP and right the 1st time, The customer wants the job done right and cheep as possible in most cases.
I've been in this industry for over 20 yrs. I started as a tech and now management.
Historically I've ran into problems using some aftermarket parts - say back when LPM was around I knew if I got a wheel cylinder or a packing kit in a LPM box, I was in for trouble. (rework was almost for sure) As a road tech I learned what worked and what didn't - The parts guy (I call librarian) only knows the part # and the margin info in most cases.

Ideally you'd select primary sources and have the part history dictate the source. In the case you let the customer decide - I'm not saying that it is wrong or out of the question.
But if you buy a poor quality aftermarket part and have to prematurely replace it. That extra 10% margin just got canceled out and you went backwards!

In most areas when options are available, I want to let our customer know his choices, I make my recommendations based on experience. If there is a gamble you try to make the customer a partner in that portion also.

I hope that helps you understand, depending on what your responsibility is. (Making bigger profits - or- customer satisfaction) that will always drive the decision unless there are standard procedures in place. Even then the rules can be bent depending on the employees.