Let me say up front that I have no real-world experience of this, so could
be missing something, but it appears to me - and I have raised the issue
with Microsoft - that the Word 12 Admin templates are copies of the Word 11
Admin templates that do not reflect the changes in the underlying versions
of Word.
From what you say, I think you are seeing the same as me, so perhaps my
observations will help you get what you want, working.
As far as I can tell, the numbers in the registry value names are all that
is significant, so, for example, Thrusday_200_1 works the same as
fHyperlink_200_1.
Your estimate of 75% of values rather understates the issue, whilst my
original querying of it was based on eyeballing the templates, giving an
even greater understatement. Many of the values used in the Template have
the wrong numbers, but as the names are irrelevant, doing them en-bloc means
that you don't realise when one value is actually changing a different
setting.
With the above in mind, it seems that the following options should have
numbers 32 greater than actually used. Note that the names are not exact,
just copied from scribbled notes, I hope you can infer the meaning; also
note that this is not a complete list. I leave it up to you, how best to
apply the corrected names in your own environment.
Headings, Bullets, Numbers, First Line Indent, assorted Japanese Closing
options, Dates, Tables.
Also, I agree with you about the groupings - more generally than just here;
the various Auto-features are intertwined all over the place.