Diverge: I expect it to happen "eventually". Thus, emphasis on actually being able to fork this from any stable release. The next two post-release planned changes and other definitely wanted changes are on the issue tracker; other technical items are buried in the source code. Intentionally introducing additional gameplay complexity is blocked by, among other reasons, having to build a library of test games to verify that various gameplay styles and starts play fast enough. Generally, if it's possible in a B-movie and doesn't break the First and Second Laws of Thermodynamics, I won't flinch at it (as opposed to its implementation). And won't flinch at NPCs doing it either.
I find the current calendar exceptionally jarring, but a number of undecided sub-issues block this so it's not yet on the issue tracker. (Introducing lunar eclipses driven by real astronomical tables appears to be an attention-to-detail task; substantial not-yet-change-planned infrastructure changes would be needed to introduce solar eclipses.) Z evolution rate would have to remain unchanged; other balancing requirements would depend on the aforementioned test game library.
Mod support: Yes, that is the intention (and not just in the survival simulation depth). Note that no further wire-in of the example tileset for the Windows/MSVC build is scheduled before 0.2.0 stable, and that no attempt whatsoever to migrate reference data from C++ to JSON has been committed as that was designated a post-0.2.0 feature.
Under the hood changes: In general, yes (a number are required simply to get the NPC AI to a maintainable state). The file count within the save directory is not on my list at this time. (I have not experienced this as a "problem", and there are technical motives for it that will not go away even after absolute locations are both introduced under the hood [for pathfinding], and mapped to real-world latitude/longitude [which should impose a still-huge limit on the file count].)