Can I...

...hide the "Save Here" for folders that have no sub-folders?

Yes. In options dialog, check the "No sub-menus for empty folders" option.

Note that this slows down Save File to since it must take an extra step to check each sub-folder of current menu folder to see whether it is empty or not. This empty folder check can be slow if folders contain lots of files and/or your filesystem is slow.

...hide the sub-folders altogether and just show the main folders?

Yes. In options dialog, un-check the "Menu" column for each folder in the folder list.

...backup and restore my Save File to settings?

Yes. Backup/restore feature is not included in Save File to itself, but because all Save File to settings are preferences, you can use general import/export extension called OPIE.

...change settings that are not available in options dialog?

Yes. Some experimental Save File to settings are hidden and not available in options dialog. All Save File to settings are stored in preferences.

...translate Save File to to my language?

Yes. Save File to translation work is done via BabelZilla.

Can you...

...add support for feature X?

Depends on the X.

You can post your feature request here. Before creating a new feature request, check the Issue Tracker that no one has requested the same feature before already.

...port Save File to to Chrome?

No. At least, at the moment (December 2011).

There are basically 3 things that Save File to requires:

Ability to create custom sub-menus and menuitems in context menu.
Read access to file system, so it can read the directory tree.
Download files.

In Chrome...

There is context menu API, but it's too limited. It's doesn't seem to be possible to populate sub-menus lazily when they are about to be shown.
There is file system API, but it's too restricted. It doesn't allow read access to full file system.
There is experimental Download API but it's too limited. It doesn't allow choosing the target folder freely.