In case anyone was wondering, yes you can, kind of.
Open a copy of SMAC
CRTL-ALT -DEL to go to task manager. Really you just want a way of accessing your desktop/files again, as you cannot alt-tab out to the desktop (to change music or, oh i don't know CHECK THE TIME o.0)
Open ANOTHER copy of SMAC. You should now have two Alpha Centauri games running.
Quit one of the games.
The other game should now be in a borderless window. You cannot use the mouse to scroll now, however, as the mouse moving along the edge will now continue onto the desktop so you can switch youtube videos or whatever.
I don't know if this is compatible with the direct draw thing above. I did not make any changes to the .ini and am running the GOG version