I use Altium on a daily basis, but haven't used Allegro since college. That said, I am fairly certain that the way the two softwares manage polygons is fundamentally different. After having to convert multiple allegro designs into Altium, I have yet to discover a way to connect traces and polygons of the same net unless you give up thermal relief by selecting "Pour over all same net objects" -no matter what settings you use. I could be missing something, but if I am it is not apparent (perhaps some scripting in the design rules would do, I haven't tried). Polygon manipulation is rather basic compared to Allegro, where everything is rather intuitive. Allegro has no qualms about letting you connect traces to polygons. In practice this means that you have different design philosophies, both of which make the same board, but converting from one to the other a pain, especially with hundreds of thermal reliefs (or if you don't have a copy of Allegro on your Altium machine, then you can't convert at all)
Practically, your best bet is to delete all the traces and then use Altium's rules to make auto generated 45° thermal reliefs. As stupid as that sounds.
Please somebody prove me wrong.