I just did these missions on a new character and I, while reached lv 45, received mk X item for Boldly They Rode. So I have a complete set with set bonus.

I think it should work this way that only when you rerun the missions at level 50 you get the mk XI.

Aren't these items also not auto-upgraded. A mk X is as good as a mk XI? You won't get the set bonus of course, but I would sure keep the mk X version for a shuttle or something.