You can also open the templaterc file and edit it. This is actually quicker if you want to do a bunch of changes.

This is how it looks with the default background fill;

And after changing it to transparency via the template dialog.
I had tried editing this before on my other computer. But I destroyed all the templates because I didn't use the correct wording for the fill-type line. This file gets automatically overwritten when you close GIMP. Not only does it save changes but apparently it also eliminates erroneous data by removing the "broken" template. So if you put the wrong information in a line in the templaterc file GIMP will completely remove that template from the file. Definitely save a copy before you start tinkering.

I changed a couple of the templates via the dialog and exited GIMP to see how the templaterc file had changed. Then I used find/replace to change the background fill, resolution, and comment settings on all the templates at once. I reopened GIMP and voila! All the templates are there and set to the proper settings.

It still baffles me that GIMP has no problem saving the resolution, the image size, and the comment when you create a new template but that it won't save the transparent fill. Clearly it knows how to save a transparent fill. Anyhow, my OCD is happy now that all my templates match my default settings.

I just stumbled across it because I had been tinkering with that curves file and started looking at the other files in the folder. But I couldn't get it right until Odin pointed me to the Template dialog so I could see how it was supposed to look.

Of course, now that I know about that dialog I probably won't need to edit the file again. From now on I'll create templates in the dialog. From there it lets you save the transparency.