The ACA doesn't require pre-boarding, that is simply a matter of convenience for the individual passenger, other passengers and for AA. If, for example, there was one person requiring extra time in each of the boarding groups and those people boarded with their group, it would mean slowing down boarding 8 separate times, rather than boarding the 8 people requiring extra time, all at once.

As to the CPAP machine, while it is unlikely that there would come a situation where the space truly could not be found, the answer is that if it came to that, you would have to make a choice as to the item which goes under the seat and one of the items would be gate-checked. Bear in mind that OH space often runs out well before BG 9 / BE, so merely purchasing Y does not necessarily get you past the issue.