In the cases I am aware of, the appointments were pretty much on time. We actually arrived early for my wife, but had to wait until pretty much her appointed time. There were others ahead. It took only 15 or 20 minutes to go through the process. This was at ORD.
Having said that, if I were doing this, I'd try to allow for a longer time in case there are unforeseen delays. Depending on where you are going, a one hour layover may not be enough. First, it sometimes takes a while to find the Global Entry office. It might take a while to get there and back to your gate. We had to ask a couple of times to find the right place to go to. The offices are not hidden, but there aren't signs all over the airport directing you to them.
The offices I've been to are outside of the secured area. You have to allow for going back through the sometimes long security lines to catch your next flight.
Planes start boarding 30 minutes prior to departure for domestic flights, and 45 minutes for international flights. Thus, a 1 hour layover is really a 30 minute break to go get your appointment done before the next flight starts boarding.
I would be leery of trying to do this with less than 90 minutes between my appointment time and the departure time of my next flight. I'd also want my scheduled arrival at the airport to be 30 minutes before my appointment time to have enough time to find where I need to go. Thus, a 2 hour layover would be my minimum. You might feel comfortable with less. It is all in how risk tolerant you are! You can always reschedule if you miss your appointment for some reason.