That 90a fuse is only protecting the rest of the system should the starter go bad. The way your diagram is showing, with the orange from alt to starter terminal and the red from starter terminal to battery, there is no fuse between the alt and batt.

To my knowledge most alternators in sport boats at least, do not charge at lower rpm’s. I know the manual for a 525efi says the alt does not begin charging until 3500rpm or so. I think you need to confirm it’s not charging at rpm other than idle if you haven’t already.