In my quick comments I couldn't explain section 88 of the Indian Act in full. To explain it in full it would take a couple of hour-long classes. Basically, it just provides for the general application of provincial laws of general character on reserve, subject to a number of exceptions.
If this bill were to pass, one of those exceptions would end up kicking in, so there wouldn't be a problem arising in relation to section 88 of the Indian Act per se. The broader issue is that provinces have traditionally exercised child welfare jurisdiction and this bill interferes off reserve there.