toponomy of placenames is discussed in the history of the ordnance survey i am currently reading. the ordnance survey generally aimed to record the contemporary spelling - and of course when they started up there was much variation. this was done by checking historical records, enquiring locally, checking lists of spellings with estate owners and clergymen, and by responding to comments on draft maps. they did of course also make many, many errors.
as you refer, the first edition spelling of pennegent matches (ish) the contemporary spelling of penegent and it is interesting to note that their spelling changed in later editions. it seems likely this would be a response to contemporary usage which correlates with your late 19th century spellings, though where the spaces and hyphens come from is unclear!
i had heard the h's and hyphens were an influence of the romantics (as in gaping ghyll etc) but perhaps in this case it is a victorian invention?