Yep. I believe it was for the release of 4, and if I remember right they just put the CD ISOs up for download with no copy protection and left any further patching up to the user.
The rereleasing was kind of a fan service. EA wanted to add some older titles on Steam, some CNC fans at EA heard about it and pushed them to also add CNC to it. I'm also now holding off with purchasing the collection with hopes of a generals remaster.. one can only hope, lol.
I think you mean Dune: The Battle for Arrakis for Sega Genesis. That's owned by EA now as well IIRC, so definitely possible. It's not C&C, but it's an RTS and plays similarly.