a) Is it a goal that all GML functions will look and act exactly, pixel-for-pixel, like they do on the Windows version?
yes, all the functions should be exactly the same code on every system except for interface ones.
b) Since ENIGMA is compiled, obviously games will not be immediately cross platform. Will you be able to cross-compile for the different platforms and produce different binaries that can be posted?
c) Will the native graphics layer(s) be used on Linux to provide seamless window manager integration? Will GTK or Qt be exposed within ENIGMA to create native-looking applications?
Native interface stuff, thus the not-linux-ness at this point.
d) Will the native sound layer(s) be used? Will this be exposed within ENIGMA to create native-looking applications?
e) Will the native input layer(s) be used? Will this be exposed within ENIGMA to create native-looking applications?
f) Will a potential build be 'certified' for particular distributions, and will DEB, RPM or other packages be available? How easy will it be to compile ENIGMA for non-binary-compatible Linux distributions? Will games produced by ENIGMA run on all or just some Linux distributions?
it produces C++ code that you could, potentially, compile any way you want.
g) How will various builds of games for platforms be shown on the ENIGMA community game database?
probably just a list of downloads with platform icons next to them, I'm not sure.