They both learned to speak English fairly well, they can both transfer all of a being's knowledge via skin contact (though in slightly different ways, it's possible that Paul is better or Roger was lying about the exact method being necessary), their species are each entirely bisexual and they both have neck orifices full of goop. It's possible that Paul was one of the technicians who worked on/tested Roger's craft, and the thing that went wrong with his ship was a cause or result of Roger's ship crashing. Any physiological differences (including Paul's nostrils and invisibility) can be explained by Roger being a crash test dummy Homunculus or having forgotten he could do that/never having noticed in the first place.