The -mod: switch really has my highest recommendation (I even rearranged my sig for it). I don't really play a mod anymore without converting it to use the -mod: switch and I haven't discovered any limitations with using it that we haven't managed to correct. My only beef regarding the -mod: switch was that CA never told us how to use it properly and it's only thanks to people like Stuie that we ever learned how it could be used and now most of the major mods use straight file overwrites .

I use JSGME as well, typically for when I'm doing incremental modding of a main build so my modded files are segregated and can be easily distributed. I had one problem with it once (I think I was was overwriting multiple mods at once) but because the underlying files should be vanilla it's very easy to restore your backups.

I would be very much surprised if something like the -mod: switch wasn't included in M2TW. It was one of the top items which the community requested in terms of modding support in a list which I know got to the relevant people at CA.