e.g., if I have $1000 in a bank account drawing 5% interest, and I take $100 and put it in an account at 3.5%, was it a good decision? From a purely numerical standpoint, no. But what you're saying here is "the 3.5% account provided useful benefits".
You are making the mistake of believing it is possible to put all your eggs in one basket, and this is simply not the way it works. I see over and over again, almost every game, that even though I've got 20 Wonders and 10 Specialists in my NE city, I can STILL see MULTIPLE cities produce a GP, because they can ALSO have 10 Specialists. And the NP city can probably have 15-20 Specialists!
If I could pack all those extra Specialists into my NE city and have 100 Specialists, okay, you'd be right, but that's not how it works.
Philosophical, Pacifism, and Golden Ages only prove you even more wrong. As you said, the effects are additive, not multiplicative.
Simple experiment: build three cities under a non-Phi leader, Bio-farm the crap out of two of them and FP the other one, and give that one NP. In one of the other two, put 20 Wonders (including MoM) and NE. Now max everyone's population. Give yourself all the techs while we're at it, and emplace plenty of buildings for happiness/health/whatever. Put yourself in Caste System and assign all your spare Specialists to Merchants. Make your production Gold too.
Your two farm cities will have a population around 40, so you have 20 specialists. Your NP city should have a pop of about 20, with 20 free Specialists, so each city has an equal number of Specialists.
Okay, let it go 24 turns, sleeping GPs as they pop up.
Now, it's time to kick off 2 Golden Ages and go into Pacifism. Move all your current GPs out of the way so you can see the new ones popping up. We kick off 2 to use 1 GP from each city, and to give us 24 turns to match the pre-GA time.
Once your Golden Age is over, take note of the ratios.
Pre-GA, you probably had significantly more GPs from the GP farm, since 20 Wonders + NE = HOLY CRAP!
But during the GA, your GP Farm's production doubled, but that of the other two cities TRIPLED. If you have the Parthenon and Forums, the difference is even larger. If you are Philosophical, it's larger still. This means your non-GP farm cities produced significantly more GPs during that time. Not as many as the GP farm, but they got A LOT CLOSER to its production.
Now tell me how you could possibly have weighted your GP farm to take up some of those slack Specialists without diminishing your total GPs or gold produced.
I don't farm that much myself, but when Sid's Sushi comes along, you better believe I switch to Rep and assign all that extra Food to Specialists for the beaker boost, and I get a lot more GPs then too, and a significant fraction of them come from the non-NE cities.