Again, Tranmere IS a place - a suburb of Birkenhead.
It is an interesting question certainly fduggan. I don't think there's a definitive answer because of the vagueness about what constitues a "place" (is it a town, a townland, a river, a building - especially one like Arsenal or Crystal Palace that doesn't exist any more?) - and the confusion that seems to exist with teams who aren't named after the place where they play but ARE named after a place. Another possible answer at the time might have been Morton, before they became Greenock Morton, who were apparently named after the name of a street.
Duncer, the Chimney Corner Hotel dates from 1871, some forty years before Alexander Irvine's book, so actually I'm not sure what is named after what!
My all-time favourite name for a football team is Hole In The Wall, who used to play in a league in N. Ireland, but I see there's at least one team of that name still going in England (!)