How can I get a more homogenous Bavarian cream?
Pinapple + gelatin should raise red flags.

Pineapple contains bromelain, a protease enzyme similar to papain in papayas. This enzyme when active will prevent gelatin from gelling. Heat will deactivate that enzyme. Canned pineapple is usually cooked enough that it isn't a problem. 

If you are using fresh pineapple (or suspect your canned pineapple wasn't cooked enough) you should cook it to at least 65C to ensure that it doesn't eat your gelatin.

Protein-devouring-pineapples aside...

The gelatin mixture is going to be much denser than the whipped cream. The pineapples will be even denser than that. In order for the two liquids to stay mixed they will have to be well gelled. Make sure the gelatin mixture has cooled enough to be very viscous. When adding the whipped cream you should fold (even though the recipe doesn't say to).

To keep the pineapples from sinking you should cut them into smaller pieces. Additionally, you might let the mixture partially set before folding in the pineapple.