The settings are more easily edited through the config program, there should be a shortcut in the Start menu (or run signalops_config.exe in the game directory).
To answer your questions, though:
- The AA setting is non-functional, we chose instead to do an alternative method of AA only on the monitor screens to optimize the frame rate. The setting is just left over in the config file, and does not show up as an option in the config program.
- alt_near_clip is is what is labelled as "Intel GPU Compatibility" in-game. This fixes some shimmering geometry that happens on Intel GPUs.
- instancing enables a GPU feature called hardware instancing, which improves the frame rate but could cause graphical glitches on some GPUs (especially ATI/AMD).
- parasite enables an alternate rendering mode that is slower but more compatible for very old GPUs, anything old enough to need that setting enabled is probably below minimum spec anyways, though. This setting is functional, but the only effect you will see is a lower frame rate.
- renderer options are gl and dx9, this can be toggled in the config program with the "DirectX" check box. DirectX mode is intended as a compatibility option, though besides a few minor graphical glitches it works just fine.