Will standard PX4 Flight Modes be available when deploying own attitude controller?

In a current project we develop our own Controll Allocation and Attitude & Rate Controller for a blended wing body fixed wing drone.

Will the Flight Modes as described here be still available?

Does anything need to be kept in mind for that?

If not: Would it be feasable the develop our own flight modes in simulink with the possibility to switch between them with a uOrb message and deploy them with the Position Controller? Does not really seem ideal to me, but I struggle to see a different workaround.

Thank you!