Did they lobby for an exemption, or is that just how the law is written?

The DMA is enforced by bureaucracy. The commission proposes that certain platforms are big enough to be regulated, and then there's a comment period/negotiation. The list of platforms currently being regulated is publicly available.

There is a hard number of users you have to achieve, its one of the reasons why iOS had to allow third party app stores but playstation did not.

In fact, Apple is still part of the DMA list with Safari, iOS, iPad OS and App Store.

I might be misremembering, but I think iMessage implementing RCS was the compromise.

Unlikely, iOS still doesn't support RCS in most European countries.

iMessage isn't popular enough in Europe to be broken up by the DMA from what I recall.

iMessage really isn't popular in Europe. Although the fact that any SMS sent between two iPhones automatically converts into an iMessage message means that there are definitely (accidental) users.