Both are simply the 30-06 necked down to 6.5, but there may be minor dimensional differences between the 2. The 6.5-06 A-square has been submitted to SAAMI, but to the best of my knowledge still has no standardization. This would be my choice if I were building one, also you will need to specify this when you get the chamber cut, no point having A-square dies and a 06 chamber.
I have a 338-06 A-square, which has been standardized by SAAMI, if the 6.5 A-square is based on this standardized case then the reamers should be very dimensionally correct, a 338-06 A-square reamer with a floating neck pilot could be used to cut the chamber and the neck/throat could be cut seperately, just ask your gunsmith what approach would be best.
Hope this helps.