I don't know if any of this will apply to Fusion as I use Featurecam, but my basic workflow for 4ax indexed parts is:
1. Model the complete assembly with raw stock and finished parts loaded in the fixture
2. Import, set the fixture model as a clamp, stock model as stock
3. Create a unique setup* for each orientation where very accurate positioning is required** and assign a unique work offset to each of them, all at the same position at the centre of rotation, but rotated as necessary.
4. Extract the machining features from the part model, within the relevant setups.
5. Probe in the first work offset on the machine, and copy the results into all the others. Tweak as required afterwards.
6. Go
* "setup" is FC terminology that effectively means a specific work offset on the machine and UCS on the model/program
** I don't usually bother creating a specific setup for indexed features that don't require accuracy greater than the machine can manage just by rotating around the centreline.