How to darken a bedroom yet let air in as much as possible

In lieu of any manufacture recommendations, I would suggest that you use the self-clean method whenever you notice a smell coming from the unit. As a related tip, if you ever notice the A/C in your car smelling bad, run it on max cool and max fan for 20minutes as this kills most of the mold and bacteria that is causing the smell; my guess is that this 2hour cycle does something similar.

I'm really not sure what the allergen clean might do but maybe run if a couple times a year.

It's probably worth noting that most A/C units don't have these functions and work fine for many years; it might be more of a marketing gimmick than anything else.

Depending on you local codes and the type of work being done, the construction contractor might be required to monitor her project's environmental impact.
As already stated, testing equipment can be expensive to purchase for private use, but Code Enforcement or the contractor might be able to help you out with a loaner of some type, or even perform an IAC test for you. Great question. Please let us know how it turns out.