Using -filemask is the correct solution. It is better to isolate your scripts from GUI configuration, so you won't break the script, when the configuration changes.
See https://winscp.net/eng/docs/scripting#configuration

Anyway, scripts do not use presets. Only default transfer settings are uses in the script.
A preset with unconditional rule actually behaves like a default settings in GUI. But not in script.

I realize I needed to manually supply them with the -filemask="" argument. I hope I'm not missing a way to have them applied automatically though, like they did in the GUI. Otherwise nevermind this post.

I'm switching from GUI to Console for automation of the Keep file up to date feature.

When using the GUI, I had set a certain default File masks with preset to be selected for all cases that got applied every time I chose to keep files up to date.

Now in Console mode, it seems these defaults aren't applied. The files that ought to be excluded are synchronized anyways.