Slap-
I think it's good. Can't think of anything that fits better.
It doesn't change the Me 163 situation : they're left as free to fly as ever (their side of the "fun" equation) so you still have to contend with em, but a handful of players can still be sure to knock out HQ and carpet the city if they play it right. There's good odds they don't make it out alive, but their target goes with em. No changes there. In that respect I think the B-29 becomes a very valuable pillar for HQ/City raids. So no changes there, no fix for what aint broke.
On the other hand the damage they do, if they hit city as well, means HQ rebuild will take long enough to be worthwhile, and on top of that will take longer proportionately with home team's resupply effort. That should be enough to open the door for strat hits at both HQ zone or at frontline factories. This setup should be near enough optimal that with a little tweaking it'd give you enough time to launch factory raids when HQ goes out.
Then adjust factory down time [edit] and airfield/vbase strat items [/edit] as needed. There's definitely a bug as Fester describes.. 45-60 minutes seems good for 100% City health, I dunno about 0%. 6 hours seems a bit long. Anyway, that's up to simple tweaking.
If this works you get a healthier system where both bombers and fighters get more gameplay. Bombers get to have meaningful targets, and fighters as well. And the mission guys probably get more of a direction to work in, instead of focusing on nameless faceless identical fields to capture.