Mission Editor version warning & bug in mission 04

I've encountered two separate issues after starting the campaign over the weekend. The first is that after the first two missions (arrival and local area fam flight) I get a warning dialog that the mission was created with a newer version of the editor than what I have and to proceed at my own risk. That's strange to me, since I'm running the latest version of the Open Alpha so I'm not sure how that's possible?

The second - and I'm not sure if this is related or not - is that when trying to take off in mission 04, by the time I get started and taxi to the runway with the other 3 ships in my flight, a group of 4 F-15's are landing. I'm told to taxi to runway 03, get there, only to have to sit and wait because they're landing on Runway 21.... the exact same runway as the one being used for takeoff. I didn't realize it the first time and barely made it off the ground and narrowly avoiding crashing - my #2 and #3 planes were not so lucky and caused an awful mess on the runway (causing #4 to abort takeoff). The second time I waited for them to land, but somehow they managed to taxi into other aircraft waiting to take off, causing F/A-18's not to be able to takeoff.

I'm not sure if I'm just doing something wrong - but it seems awfully strange to me to have both launch and recovery operations happening at the same time in opposite directions (i.e. taking off INTO recovering aircraft) - especially using the exact same runway when a parallel runway is available.

Lastly - and this is mostly just an annoyance to me - does anybody else get annoyed by the fact that ATC never specifies L vs R when clearing you to a runway when there are two parallel to each other? Do I get to just pick which one I feel like using?