Exactly. Naming change of mediavps mod folder was intentional. You would have had a ton of broken mods and campaigns in your hands if that hadn't been done. The bottom line is that anyone should be able to play mods and campaigns as-intended regardless of what mediavps version they were built on. Mucking around with mod.ini's is not recommended and should not be done unless you are sure the mod or campaign in question actually works with 3.6.12's without debug errors. That is a problem for authors to handle and issue an update, not end-user.
Next major update of mediavps should again use version number in the mod folder to avoid mods and campaigns designed for 3.6.'12 from breaking. In best-case scenario you only have current and previous mediavps installed. But of course, that all depends on authors to keep their mods up-to-date, which is not given.