For one you can place enemy zones manually (which is good because you can base them at strategic points rather than just allover the shop).

I would guess this version is being updated.

The "Modified" version includes features that are tied to other mods, RHS Escalation for example. I'm trying to keep DUWS-R a "pure" mission for ArmA. While I do understand there are many people that love things like RHS Escalation and love features in it compatible with DUWS there are also people out there that want a non-modded experience. I'm really hoping to make DUWS-R a great "base" for all of those other mods. That is one of the main reasons why DUWS-R was forked from the original DUWS and not any of the "Modified" versions. That said, the team is taking features and bug fixes from the various modded versions and incorporating those into DUWS-R.