1)

If I save a spreadsheet as a template, chances are I'm saving just the
underlying calculations but not the data itself (i.e. only part of the
spreadsheet is saved). When Hob asks me if I want to "Save As Template"
the project on which I am working I have to wonder which part of the
overall configuration is going to be saved, and which part is going to
be discarded?

Perhaps "Save Project Configuration" would be a better wording?

2)

Also, the ability to save the project's configuration is only available
(I believe) at the end of the workflow; when a successful image is created.
Although a given configuration might not bake correctly I think it would be
nice to be able to save the configuration as I go along, seeing how the
entire process takes so much time.

3)

Relating to Bug 2934 it would be nice if the things that are saved as part
of saving the configuration would update the project's files instead of
creating Hob's own files which are separate from the project's.

Maybe this could be done automatically instead of needing an explicit save
action on the part of the user?