Regardless, it still confuses me - do I just need to align the front wheel over a bit?
No.
The post mounts on a post mount fork are positioned further inwards then the IS mounts on a IS fork. The brake will end up being in same position on a PM fork as they were on the IS fork with the adapter.
A 100mm travel fork should be OK on your bike, it's probably not a good idea to get a fork with any more travel then that.