In the broadest, most general sense, you can do anything you want to do. If it were my project, I would first measure the pistons and cylinder bores to determine if the clearances are going to be within spec.
Why?

I am not concerned about that the (aprox) cylinder size IS the same and bmw has 3 to choose from. I can easily measure and order appropriate piston size. I am concerned about /6 head and valve clearance as the part # is different.

Well then, there are 4 things to consider.
1) contour of the domes of the pistons.
2) diameter of the valves at the seat end.
3) cam lift.
4) cam duration.
So far as I know, these technical specifications are available in the factory service manual.
If the pistons have different part numbers, but the other three are the same, you'd probably be O.K.
I will look into this in my parts manual and report back at a later time.
There is no interchange manual for airheads that I know of. One must divine this info from the parts manual and the factory service manual.

O.K., in my 1980 parts manual, on the piston pages for R90/6 and R90S, the rings, wrist pin, and circlip have the same numbers. The piston numbers ARE NOT the same. However, the part numbers for the intake valve, exhaust valve, and the cam ARE the same. It appears that the difference for the cylinder head assemblies is the intake manifold. Read in to this what you will.

Both valve and cam numbers are also indicated for R75/5 and /6.

Question; if you intend to order pistons, why not order pistons for the R90/6?

I am concerned about /6 head and valve clearance as the part # is different.

You can gauge this with ease by installing the head after locating numerous quarter inch balls of Play-Doh around the piston crown. Simply run the piston past TDC one time. Do the same to check valve-to-piston eyelash clearance too. You need at least 1/10 inch clearance due to rod growth.

Hope this helps.