Technically they're mods. Versions would mean that they're steps on the ladder the original devteam was going up on the way to a finished product, sort of like how Version .25 is less developed than Version .50, or how CVS IVAN is more developed than .50 IVAN. This may seem odd or unintuitive to a person who's new to tracking this sort of thing and is experiencing this as their first roguelike (which you may or may not be, but it sounds like you may be new to this sort of thing), but basically roguelike designers don't generally have the luxury that major company game makers have of putting forth the publicity necessary to ensure that when the game is done, it actually has an audience who will buy it (though even then, especially in the case of PC games, there will very likely be patches that change the version of the game from 1.00 to, say, 1.02 or 1.03). Most roguelike developers, instead, go ahead and make their games bit by bit, releasing semi-finished products and then taking in suggestions and bug reports, which allow the designers to both fix their game and possibly improve it in ways they weren't originally thinking of. Since the developers of roguelikes also generally live off of or persist in developing roguelikes instead of getting a normal day job, this also serves as a quick way to tell whether the game in question is a good one or not; no donations = no interest, and they need to find something else to work on (although some might decide to stop entirely if the no donations situation persists).
Mods, on the other hand, are the work of fans of the game who have taken the original game files and, being unaffiliated with the original game designers, modified them in certain ways. In this particular case, the confusion is understandable as development on the original game has come to a complete and (sadly, despite Kahvi's earlier assertion that he might be able to work something out with holykiwi) utter halt, leaving mods to be the only actual new content relevant to IVAN.
As for what's different about them? Why not try downloading them and playing for yourself? There's also bound to be version documents that will tell you a lot about the particular changes that have been made.