I would pinch them off the flowers and allow whatever energy left from the cutting to go toward rooting. Cross your finger and hope the cutting will root before all the store energy used up and the cutting dry up and die.

Tony

there are also new buds that are developing out of the dark
in addition to the buds that are already there.

Should i let the new ones that are forming remain?

I would pinch off all flower buds from you rootstocks. Callery are pretty tough but as Tony mentioned they only have a chance to grow for a short time.