Native. EDuke32 requires DUKE32.GRP. If you have installed Duke Nukem 3D, you will find this file where ever you installed the game to.
When launching eDuke32, you will get a launcher. Make sure fullscreen mode is enabled. If it is, all of your resolutions should be available.
The auto-map has some aspect ratio issues that prove problematic.
First, 16:10 is the only aspect ratio where it works correctly. You can tell because when you rotate it, other aspect ratios have a skewed look, as objects change their dimensions as they rotate (what used to become a square turns into a rectangle as it turns 90 degrees, and back to a square as it turns another 90 degrees).
In 4:3, the map is both hor - and horizontally squashed. It's like it gets horizontally squashed and then it zooms in like that was supposed to compensate.
In 16:9 and wider, the map simply stretches horizontally.
The map is used constantly throughout gameplay, and IMO, this distortion goes beyond an aesthetic fault, so I have to consider this a consequential flaw.
FMVs are stretched. There are also some static 2D screens in between episodes, and they too stretch.