Yes, enable it by linking a version of FFmpeg with GPU acceleration to Auto-Editor and setting the appropriate video codec.
Use --my-ffmpeg or --ffmpeg-location option for linking.
Compile FFmpeg with the appropriate flags and follow the relevant instructions.
FFmpeg Compilation Guide
Remember to set the export codec in auto-editor. auto-editor --video-codec.
Note that the resulting build is legally undistributable.
If you want to export to a certain codec that is compatible with your GPU, yes, in some cases, it will go noticeably faster, albeit with some slight quality loss.
However, in most other cases, GPU acceleration won't do anything since analyze and creating new media files are mostly CPU bound. Given how relatively complex enabling GPU acceleration is, it is not recommend for most users.