For full game runs, the categories are called "Newest Version" and "Any Version". Newest version applies to any V1.03 version as stated in the rules. This is any version on PC currently, and any console version that HAS been patched. Unpatched console versions can only be submitted to Any Version.
Note that these category names mean that if another patch (of any significance) comes out, all current runs under Newest Version will have to be moved to Any. I consider this scenario unlikely at this stage however, I think any patches from this point onwards would probably only do things like prevent soft locks, which wouldn't need to be separated. I'd be surprised if they re-patch out Studiopolis 2 glitch, for example. However until we know for sure, this is the best option.
For the Individual Levels, sub-categories have only been applied to levels where the version actually matters, in order to keep as much competition together as possible. As such methodology is being used, the categories are referred to as "V1.03" and "Any Category", as any further updates would only be applied to the levels they matter in. The levels they have been applied to are: With All Characters: Chemical Plant 2, Hydrocity 2, Titanic Monarch 2 With Knuckles: Green Hill 1, Studiopolis 2, Flying Battery 1, Press Garden 1
If I've missed any levels, or if I've misplaced any runs or something, please let me know, and I'll be able to correct it. Also note, as mentioned in the rules and as the name implies, you can submit any times to "Any Version", even if you have already submitted them to the newest one. So you can double submit if you wish, however it's purely up to you (but I'll probably double submit across if it's the record on both)
In the future there should be support for variable+ for subcategories, so games that use difficulties can have Easy+Normal+Hard, Normal+Hard, and Hard for example. It can also work on this leaderboard system to let all the "latest version" runs also appear on the "any version".