Since the A-League Championship is on September 20th, that means if an A-League team makes it to the US Open Cup final they'll have off until sometime in October? If that's the case that sucks for any A-League teams that make it far.
I don't think there are any dates out yet for this year's competition. Yes, it does suck for the A-League teams. Since MLS began, the final has been post-MLS Cup all but one year and - voila! - the year that it wasn't (in 1999, the game was on Sept 15) - Rochester won the Cup. The only other time an A-League team made it to the final in the MLS era was in 1996, when DC beat Rochester 3-0 in an Oct 30 matchup. This year, it might be harder to have it be a post-season final since the MLS championship won't be decided until November. Perhaps the USOC final will be earlier.
USL US Open Cup Qualifying will end on May 26th. There is still the MLS Qualifying because 6 clubs will get automatic bids while the bottom four will probably duke it out using their regular season Schedule doubling as qualifying matches for the final two spots in Round 3 of the US Open Cup.
Actually, the final was supposed to be during the MLS and A-League regular seasons in 1998, too, but a hurricane had other ideas and necessitated moving the final, and delaying it, until after MLS Cup.