I noticed that the demo galleries included in the download use different thumbnail sizes leading me to believe that whatever the size thumbnails are put into the content folder are used. However, the different thumbnail cropping modes seem to be part of the theme which I assume applies to all the galleries.
Thumbnail settings are part of the CONFIG, not part of the themes ...
You can change thumbnails per folder by following this process:
# Go to admin -> config -> thumbnails.thumbnail, and make your settings for the thumbnails you want to create. Save, and navigate to the folder where you want to change thumbnails. Click "recreate thumbnails in current folder" (unless they are created first time when you visit the folder).
Repeat this step by going to config and changing your thumbnail settings. Go to manage any of your folder and change thumbnails appearance.