Digitalam I wouldn't say there's any con. It might not be easy achieve, but if you can get this to work you'll probably know enough about both sides to know if anything will cause an issue to your particular use case.
In any case you should develop your custom Flarum authentication as a (private) extension and use our PHP extenders so you are able to update Flarum without your custom logic potentially breaking on each update.
Using a custom middleware to set the request actor should be all that's needed to interact with the Flarum stack. Then that middleware can handle all the custom logic.