Sure, large animations are the primary use for binary. We totally recommend that.
What we don't recommend is updating your runtime for new features right before you need to ship, 'cause it takes an unknown amount of extra work on your end.
I'll show Nate your suggestion.
But I think he'll still recommend saving an Export settings file (json) per project.
That allows you to just edit the text in that json so you can change the input/output paths or adjust the export settings, instead of having to open each spine project in case something changed. It's an upfront cost if you weren't doing it already for sure, but saves time down the line. Not sure if that's a perk for you.
I'm also not sure what export settings projects actually store. But I'm sure path typos aren't a problem if you don't actually type them manually.
Unless you're a mac... Can you copy paths as text in OSX?