Yeah, it is kinda confusing you are right.
Maybe swapping the version to 0.0.3 in the next update and addressing it would be a better idea then.
And thanks for the tips!
There is no dedicated system out there for versioning, just to ease your worries. All software, games, hardware anything has completely different systems that made sense to them at the time. However, I think you have a good basis for changing how your revisions/updates work in relation to version numbers now since you're so early in development.
If we go based on you have two releases and a third coming up I'd do something like:
ALPHA 0.00.01
ALPHA 0.00.02
ALPHA 0.00.03
Etc. Eventually when you feel your game is FEATURE complete as in all systems are in place and will not change then you move on:
BETA 0.01.34 (An example). If the numbers need to go up past two digits due to either fixes, updates, whatever; just do:
ALPHA 0.00.112
What's more important is that it's clear what version you are working in and what version people are playing. I'd recommend, at least until full release, having the version number show up as part of the title when you launch the game. I'm not sure if you've already done it but since you're using Ren'Py I'd make sure that you've made the games' title the actual process name and be what shows up along the top when in 'Window' mode or when hoving over the taskbar (I'm using Windows logic here as it's the most common OS however this would be similar for Android, Mac, and Linux just different titles).
Anyhow sorry to ramble on there I just suddenly felt like throwing my 2 cents into versioning. I've only played the very original release myself but the art direction is magnificent. I do hope you keep going. If you need any assistance with editing your writing feel free to reach out to me, I've been known to dabble in editing (Even when the writing is already within Ren'Py scripting).