Did I read somewhere that you are not supposed to use the B/BC/CH in different uppers?

If so, why is this?

I think it has something to do with headspace .... .... but i'm not really technically knowledgeable about the matter.

Others will chime in soon i'm sure.

I thought it was OK to swap carriers anytime, and bolts when barrel/bolt are fairly new.  After many rounds, you're not supposed to swap bolts anymore.  

Someone will come with the absolute right answer soon!

There is no issue with using a bolt carrier or charging handle in different rifles. Bolts are another story. If both the bolt and barrel are new, this usually isn't an issue because if the parts are in spec it dosen't matter who made them or when. If you switch used bolts between rifles you MUST headspace the parts to be sure you don't have any issues. Every rifle wears at a diferent rate and it takes very very little excess or short space to cause a KB or other issue.

can someone explain the mechanics of how a misaligned bolt & barrel extension combination could cause a KB?

I put a used Bushmaster bolt in a used DPMS barrel after my Colt bolt had some issues.  Then, I swapped the DPMS barrel with a brand new Wislon a little while later.  I haven't had any issues, FWIW

It's an issue of headspace. As a general rule headspece increases over time. As you use a bolt\barrel combo you get wear to both the bolt face and the locking lugs. Since every different manufacturer produces parts to the same general spec, all parts should interchange. The problem is you have no idea if the bolt you just got was produced at the beginning of a production run on freshly calibrated like new equipment, or the last bolt on a piece of machenery badly in need of rebuilding.

More on headspace. If it's too short you get a cartridge jammed into the chamber with the case neck stuffed into the begining of the rifling. Too long and you have too much room at the head of an unsuported case. Short headspace causes excessive chambar pressure, long headspace allows too much pressure to breech the case head and blow back into the action, or your face.