The 90 mm uPVC (u indicates unplasticised) storm water pipe is 90 mm OD. The 100 mm pipe is 110.2 mm OD.
The builder would have noticed what pipes they were IF he saw them being laid because DWV, as well as being noticeably bigger, is also a different colour.
He probably just referred to the plans IF he didn't see the pipes but I can only guess. His correspondence however indicates that he was expecting the plumbers to lay 100 mm pipe. It then follows that the plumbers would have been paid accordingly IF what the builder has indicated in the correspondence is a truthful account.
I would love to know what you paid for and what the plumbers were paid for. At the end of the day, the plumbers should have used 100 mm for compliance but didn't, they used the el cheapo and not compliant as per AS2200 flimsy 90 mm uPVC storm water pipe instead.
As far as the slab goes, the plumbers have no excuse to have not noticed the heights when plumbing the pipes.