Sounds interesting. I would agree that the separate basing for pike and shot elements is not necessary, nor particularly useful for most purposes in the 17th century.
Prior to c1530 however I don’t see Pike and Shot operating sufficiently interdependently to justify basing them as one unit. Shot grew in number but operated at least semi independently, and usually only successfully when esconced behind some sort of fortification. I wouldn’t feel I was even vaguely representing the tactical choices commanders had if I arbitrarily lumped the two together in that period.
Between c1530 and the 17th century there is a more flexible picture as shot numbers increase and tactical mechanisms between the two arms developed. By the resumption of the Dutch 80 Years War I’de be happy with permanently mixed bases, before that I’d be wary.
Of course if your rules work to your satisfaction with those methods that is absolutley fine.
I think I will continue to operate the two independently in the earlier period however.