Thanks very much for your interesting , scholarly and authoritative post and the registry set material. In parts, I think it complements Doty's book on the Soho Mint. One very minor point, I was slightly surprised at the, at first reading, absence of reference to Sierra Leone (Company) coinage.
However it will take me some weeks , to make time, to fully assimilate it all. Your comments are very insightful : i agree about Peck generally. I try to respond to your questions and comments with brief descriptions of my experience on just the Peck 1788 -1799 coins below.
I aim to collect Early and Late Soho coins of Peck's C 1(a) and C2 (a) - (n) excluding (b) and (k) in different metals. Gaps are sometimes filled with Taylor restrikes. My comments on the NGC census were based on 37 coins of 1788-1797 of which 11 were PCGS graded and required some classification input from me.
On your 1 , labelling and mis - labelling is an issue: a notable current mis-labelling example is a Pr68 1799 halfpenny , in a Heritage August auction, labelled as a farthing, corrected by Heritage.
On 2, nice to read this , I agree, but NGC is not immune either.
On 3, I agree about UK (Europe). but relative rarity for coins TPG rated 60 or above (say) may give some useful partial information about relative rarity your P-965 is a very good example but so is P-966 in Brown Gilt.