It's not a deliberate design no. Though your demesne galleys should be about twice as high in PB as vanilla, as I don't change the number while at the same time doubling their capacity.You'd think I'd have thought of that, having spent most of last night digging through that file for the wiki
Another random annoyance:
Generally I've found that ships available from my personal castle holdings don't scale well enough to support my demesne levies and my retinue once I hit about Kingdom size or a bit bigger. It's sometimes the case that I want to only utilize retinues and personal levies in a war, and don't have a way to do that without either hiring a merc fleet or a raising a vassal navy (which defeats the purpose). Would it make sense to add a few galleys to castles or castle buildings so that personal fleet can scale with personal levies and retinue, or is this intentional?
However, it is a design decision in vanilla that most galleys come from cities, not castles. So call them up from your vassal barony-level cities if you need more.