Everytime you open up a section of the game it's a bit like disassembling a car. You need to remember where every piece goes, and more you need to make sure none of your pieces get mixed up with the team that's disassembling the car right next to yours. In short, it sounds easy and fast but it is nothing of the sort.
Personal Challenges are currently working, although I would argue that an imbedded "Or" condition would optimize them for Co-Op Compatibility. At the moment, this isn't on our roadmap, so it's not going to be prioritized. I'll keep looking to push it, but it's not a thing at the moment.
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Your inferrence is that Subs are taking away from valuable Personal Challenges time, but the reality is that these are completely different teams doing completely different things. Again, it's not a simple fix.