It was probably purposeful on the part of PyTom, the main author of Ren'py. I obviously can't speak for him, but I would guess that it has something to do with what he sees as the "primary use case."
To be frank, you're the first user I've ever had comment about the default setting on this particular feature. Since the vast majority of the developers don't make any modifications to the preferences, I'd bet dollars to donuts that most of them aren't even aware of the fact that it can be set either way.
I don't mean to offend in any way, but my sense, based on my own personal experience, is that you are in a very small minority in terms of caring about the default setting on that particular feature.
I would agree that doing something like that is not particularly user-friendly. Nor is making the preferences ONLY available from the main menu, as opposed to having them be available in-game. Nor interfering with the ability to save in-game. All of those are things that, IMHO, make Ren'py a very good engine from a user point of view. But blasting developers because they don't change one particular setting (which would affect all users) away from the default to suit your personal preferences, when it's a two-second operation for you to adjust them to your liking, well, to me that's a bit harsh. Just my $0.02.