Not a programmer, but version numbering is actually pretty simple. Given XX.YY.ZZ:
XX is the major build number, which is 0 until a project moves out of beta and has a full release, at which point it becomes 1.
YY goes up with every revision of substance (it often gets started as 01 rather than 1 because of how computers alphabetize things), so that's the number that generally goes up with every build on itch.io.
ZZ is typically used for hotfixes, tweaks, and revisions, so v0.01.2 has the same content as v0.01, but is more stable/polished.
Hope that helps, even if you prefer linear numbering.