Possibly. However, you may be missing more than you think you are - 68.2 was the old version of the game before the new faux
First of, you cannot brick a Windows installation by changing values in HKEY_CURRENT_USER\SOFTWARE branch.
Second, I think the location of the game's save data is stated by the author himself. The point was not that it's there, but that it is compatible and easily transferable.
You are basically saying not to mess with anything and play as intended. I'm saying - fine, but here's another option. It worked for me and saved me time, IMO it will just as well work for you if the need arises.
An aside about storyline and reconfiguration changes:
A cursory glance at save data from 0.68.2a and from 0.89.8b does NOT reveal major changes. Actually, it seems there are no changes in data structure at all. That in itself very strongly implies compatibility, even if some actual restructuring of quests took place.
And IF there are changes, they all must be trivial just by virtue of the game being basically linear. It's just a bunch of scenes and the flags for their availability, and some flags for major decisions. No need to overcomplicate simple matters. The reason why the author didn't provide a compatibility option is a mystery, but it's definitely not because it's difficult.