As far as I can remember, 1.01 was the only bug fix release. 2.0 added the protection against modding (which can easily be modded out). And 3.0 is just the Steam release, which changed some minor things and did some reorganisation of code, but didn't seem to actually DO anything... If you want I can send you a 3.0 .exe which works without Steam to test.
However, modding protection or not, each .exe version has subtle code differences, which can turn into huge differences internally. Either by accident, or very possibly intentionally, the 3.0 .exe is hugely different to the 1.01 .exe (I don't think I've ever bothered looking into the 2.0 one, really) not just in what was added or changed, but how the code was compiled. Perhaps they used a newer compiler or changed some optimisation settings, either deliberately to make the .exe's more different as extra modding protection, or some other cause.
This means that the memory addresses we can use to modify a running .exe can't be considered valid on any other version - on 1.0 the address 0x438E40 points to the start of a function which awards money and health for cheating, yet on 3.0 it points to the 3rd/5 byte in an unknown call which is part of the 'Path Finder' system for vehicle road navigation - far off. 1.0 exe's are the most documented, so they are what most mods are based on, for simplicity, compatibility and capability.
Unfortunately, it's not even possible to simply create some sort of tool to intercept and convert addresses from one game to another, as sometimes what is being written there wouldn't even fit. So the more plausible option is to bring these fixes back to 1.0 through more mods, or wait until 3.0 is as documented as 1.0 and attempt a universal switch, which would be difficult and would require mods who's authors are unable to convert them being forgettable enough...
But still, if I had to choose between an .exe with a bunch of fixes and an .exe which supports lots of additional content and a few of those fixes for good measure, I'd say stick with the 1.0