I've noticed that at some point things changed so that changes in the
Customizer count as changes in the model - the tab bar has a *, and
attempting to close the file prompts you to save.

I understand that some people may want to save Customizer sets, and I
might even want to sometimes, but most of the time if I'm changing
something in the Customizer it is a one-shot to create some specific
combination and I don't want to save it.  That means that I find the
"document has been modified" treatment to be confusing, because I didn't
change what I think of as "the document".  It worries me - did I change
something and forget about it?  Did I accidentally type something into
that pane?

And I see that if I've done something with the Customizer and saved, it
clutters my directory with a .json file that I don't want.

I'm not sure what I would suggest changing, since those people who do
want to save their Customizer settings would presumably like to know
when they're about to lose them, but I thought I'd bring the question up
to see if anybody else has an opinion.

I also think I see a bug:  if I use [-] to explicitly delete that new
automatically created parameter set, that too counts as a change, and
when I save... it does not update (or, preferably, delete) the .json
file.  When next I load that .scad file, the deleted parameter list is
resurrected.  I'll file a bug.

The flip side of this may have bitten me (just a little):  If you don't
care about the parameter sets, you're more likely to say "no, I don't
need to save, it's just complaining about the parameter set" when you've
actually made a substantive change.

One piece of the puzzle may be for the "do you want to save your
changes" dialog to make a distinction between "you've changed the model"
and "you've changed the parameter set".

Torsten:  yes, that (default parameter set is transient) was one of the
variations I was thinking of.  I think I wrote it down and then removed
it to keep the message simpler.