Bump. Still looking for an answer for the question above.
I'm still waiting on a clarification myself. Honestly, neither option feels particularly acceptable once one takes some edge cases into account, so I'm running it up the chain.
Cool. I’m just looking for something that makes sense. Thanks for the update.
Aaaaand, ANSWERED!
The official answer is that there are three things which are handled "by location", meaning you change all of the things in that location with a single increment of time. Those three things are:
Heat Sinks.
Omni Podded items.
Armor.
The reason it took so long to get an answer is because I referenced the StratOps errata when I wrote the original question, but the answer already existed. It's in Campaign Ops, p205.
So now, to give an example, if the base time increment of 1 box of armor is 10 minutes, and you want a REFIT (not a repair) of the 20 points of armor in that location, the base time to refit will be 10 minutes (10x1), not 200 minutes (10x20). Same with Omni-podded weapons; if you've got Ryoken with 6 ERMLs in the right arm, and want to pull all of them and exchange them for 6 ER Smalls, then pulling them would be 15 minutes (15x1), not 90 minutes (15x6). Note that this applies to refits, not repairs. Armor must still be repaired box by box, and omni-podded items must be repaired individually.
I'll be cross-posting this over into the rules thread as well, since it's a fairly hefty clarification.