If I use a quick tm on machamp w bullet punch an I guaranteed counter

You can't get Bullet Punch again so yes, you are getting Counter for sure.

Yes. It's a 100% guarantee to get the other move.

Now if it have KC it would have been a 50/50 between BP and C

Does anybody know how this works for charged moves?
May i be stuck changing between two unwanted moves wasting many machines, or is there a cycle of three moves so i get my wanted move for sure after the second try?

I tried experimenting on my charge TM, i used two on my Flareon. Initial charge move is Flame Thrower, then i use the Charge TM twice: first result is Fire Blast, 2nd result is Flame thrower. So i guess it's random.