You seem to be mixing several things together that really aren't a problem.
Firstly, we need only consider cities that can be irrigated. I only build farms in those and workshops or cottages where irrigation is not possible. My workshops will be the same as yours except they lose 1 hammer from CS - a small price to pay given the few workshops I use and the relative rarity of such cities.
Your calculations on a per tile basis is leading you astray and your analysis is not giving correct outcomes. We need to do calculations at the level of a city since the whipping and drafting restrictions are affected by city size and only a limited number can be used in a given time period without incurring excessive unhappiness.
So let's take an example city and study it over a whipping-drafting cycle of 10 turns and then compare its output with a workshop alternative. The city I have chosen is distinctly unimpressive at first sight and many players would not even settle it. It only has access to 6 tiles, 3 grasslands and 3 plains with remaining tiles in the BFC either useless or belonging to other cities.
Early in the game (pre Biology / Communism) this city produces +5 food and up to 4 base hammers (5 with forge). Under Slavery and Nationhood it can be used to draft a musket and whip a cannon while putting spare hammers and overflow into a mace. Drafting at size 6 costs 15 food. A cannon with 5 hammers invested will be a 3 pop whip with significant overflow of 23 hammers which carries into the mace. If we assume a whip from size 7 to size 4 it costs 14, 15 and 16 food to regrow which takes 9 turns and there is some loss of hammers from the plains farms. So over a 12 turn cycle we whip a cannon and draft a musket and put hammers into mace. The mace will get 23 hammers and a varying amount depending on how many plains farms are worked that I can't be bothered to analyse in detail.
Without SP to boost food there is no need to do a workshop analysis for the city at this stage.
Later when we have Biology and Communism the same city gets a huge boost of another 6 food and the 10% from SP. We'll assume Kremlin has not been built, initially. With +11 food the city can support the drafting of a rifleman and 3 pop whipping of a cannon on a 10 turn cycle and the excess food is used used to run spy specialists. The intelligence agency and jail have been added to the city to provide slots and EP %bonus. Let's analyse the food usage:
So comparing the two cities we get:
Workshop: 320 hammers + 68 draft hammers = 388 hammers
Slavery: 121 + 50 + 110 = 281 hammers + 198 EPs + 110 beakers.
Running an engineer instead of a spy for 10 turns would add 30 hammers for loss of 90 EPs and 13 beakers.
Now let's add Kremlin into the picture and with Assembly Line and Artillery increase the hammer cost of the troops. The workshop city might build a factory and coal plant but so could the Slavery city. For the sake of the comparison we will assume either they both do or neither do and the production bonus essentially cancels. The same can be argued for the use of PS, which is usually adopted for WW reasons rather than the production bonus.
The food analysis for the farmed city becomes:
So comparing the two cities again we get:
Workshop: 320 hammers + 10 from part time engineer = 330
Slavery: 182 + 50 + 140 = 372 hammers, plus 117 EPs and 65 beakers.
In peacetime the two cities can be run to produce wealth and EPs etc. instead of hammers and units.
The farms will now provide enough food to run an average of 5.5 spies, thats an alteration of 5 spies with +1 food and 6 with -1 food and the pop being whipped or drafted away periodically. At size 11 the city can support 5 spies giving 45 EPs and 25 beakers per turn and build 5 wealth for a total of 75 output.
The workshop city can build 33 wealth. The farms / specialists are more than twice as good. The workshops would almost certainly build the factory and coal plant in this situation (costs 450 hammers) and then the wealth will increase by 18 to 51 so it still loses out heavilly even after a lot of extra investment.
I was going to add an analysis of a simple coastal city with a single clam and 11 coastal tiles and no other useful tiles (ice or tundra perhaps). But suffice it to say that whipping a battleship every 10 turns or so (Kremlin, Drydock, forge and SP) should impress you enough to realise that the CS/SP civic combination does this little gem no favours. Between battleships it can either draft or run a few spy specialists making a flexible use of its limited 5 food surplus.
Overall, as long as your game is orientated towards the effective combination of espionage and warfare then the combination of Slavery, Nationhood, SP with Kremlin and spy specialists beats workshops with SP/CS by a considerable margin. This happens over a long period of time during the critical transition from the pre Biology period when cannons and muskets are the best available troops through to the late game when whipping tanks and other large value items just makes the Kremlin more efficient. It's more flexible, you get a bigger army quicker and have lots of espionage to ensure you know what the AI is doing or to steal techs or disrupt civics and religions. And finally many more of your cities can have useful production both for their own infrastructure and extra units, flat land for workshops is not needed so many more city sites are useful.