You may have found a solution to this now but I thought I'd post my solution here, in case anyone searches for this and it's helpful for them.
Firstly, Batcher does now allow loading preset files, which is good!
To create and load a preset:
- Configure your levels , *making sure you have the 'Linear' button checked to ensure compatibility with Batcher*
- Click the button at the far right end of the presets bar (tooltip: Manage presets)
- Choose 'Export Current Settings to File'
- Save your preset file wherever you like, *with the .gtp extension* e.g my_levels_preset.gtp
- Load your preset file in Batcher and run
