Regarding the MIDI controller - yes, you'd be able to manually sweep the filter as you've described.
I can't comment about Protools or Logic, though, as I don't use either of those. There have been some compatibility issues with third-party software with the Arturia synths. (In fact these forums tend to be mostly people blaming Arturia for things that work perfectly well until you interface with some other piece of software that Arturia didn't design and have no control over.) Amendments to the Arturia synths appear periodically, but that work is of course fitted in with the new development work they're doing - and have to do to stay viable as a small company.
If you check the FAQ on the main site I think there are known issues and maybe workarounds, but as none of these things have ever affected me I haven't checked.
The MIDI learn feature is described in section 4.3.5 of the Manual, page 60, BTW. I'm using the hardware controller of my Virtual Korg MS20. Several people have mentioned a Behringer controller that has quite a lot of controls at a good price.
Thanks for your comments on Rainfall in Kyoto. Yes, it's the only completely MMV piece I've done, though I've used the MMV on a lot of other recordings, mixed with other instruments. I've also done a completely 2600V piece that I'll put on the site at some point, and I'm intending to do a piece completely with the MiniMg V as well.