While I personally feel the same way (if for no other reason than, as a developer, I'd want my versions to sort out logically and trivially)
As a developer, it
is a logical sort, albeit not a mathematical one. It's called x.y.z versioning, with each symbol corresponding respectively to major releases, minor releases, and patches. As their names imply, major releases are reserved for a huge change in functionalities (a 1.0 usually being the first proper public release of a finished project), minor releases are for more modest implementations and modifications, while patches are mostly bug fixes. They're all numbers and incremented separately, and don't work like decimals. Hell it's not even that rare to also have letters for patches.
Most softwares have it or a similar form, it's just not front and center since it's not really a useful information for consumers. And I guess that's also why some games on this site use chapters and parts instead, it's probably less confusing for people not familiar with the convention.
... If I had a nickel for every time I explained x.y.z versioning in this thread, I'd have two nickels.