This is just a consequence of the PK being a clustered index in InnoDB which has both pros and cons. One of the big cons is that all of the columns of the PK are implicitly added to every secondary index as the row identifier. That isn't a big problem if your PK is a single column int, but if it's multiple columns, that often results in unnecessary bloat in your secondary indexes. Ideally (as in, dare I say, MS SQL Server), you'd have the option of a clustered or non-clustered PK for your table so you could choose the optimal index structure for your workload on a per-table basis.