Following a GOG conversation, I decided to try to see if I could get Deus Ex GOTY, which I have at GMG, installed as a DRM-free game.
I’ve read that GMG uses Securom for all games, and it looks like this is the case. Downloading Deus Ex on my PC it asked for an unlock when it ran. I copied the entire game directory to my laptop, which doesn’t even have Capsule installed, then downloaded and installed New Vision. I had to delete DeusEx.ini and User.ini to get the game to run, but once I did that it ran without a problem.
So there you have it, a DRM-free copy of Deus Ex downloaded from GMG. Not as trivial as getting one from GOG, but if you intend to install New Vision it’s not really any more work. You have to have Capsule installed to download and install the game, but it’s not necessary to run it later, and the copy can be backed up easily.