Yes, related party transaction stamp duty waiver only applies to transfers between companies. Not individual to companies and vice versa. Besides, why do you want to transfer the property from an individual into a the company?

The developer cannot levy any charges to execute memorandum of transfers for cases of perfection however they can levy charges on the execution of same if they have agreed on effect a transfer directly in favor of purchasers (where subsale transactions are involved)

Even so, it depends on whether the property is categorized as commercial or residential. For the former, an administrative charge of between "1% - 2%" on the current selling price or the price in which you acquire the property (whichever is higher) is applicable.

For residential, a confirmation fee of RM53.00 only can be levied. Under HDA, the developer cannot impose any other conditions.

DOA is when the property is still under master title.
MOT is when the individual document of title to the property has been issued.

Assuming the subsale transaction of the intended sale has been completed, only B gets to pay the nominal stamp duty as B would've paid the full stamp duty for the assignment contemplated in the subsale transaction.

A will have to pay the full of its share in the property valued based on A's initial purchase price.