I have problems with several of the rules. There are clearly some hidden assumptions that would be better stated explicitly.
Rule 2 Build Granary is obvious. But what about a courthouse? In an empire with say 13 cities and if this city is quite a long way from the capital this is just as vital to avoid unnecessary losses. A size 12 city in that situation can easily cost 16 maintenance per turn so a courthouse will save 8 gold and add 2 EPs. In the early game before many of the cottages are villages whipping a few pop to build a courthouse should be added as a conditional 2(a).
Rule 4 slave another worker in a CE city
If the city has silly production and plenty of food maybe but a low food, low production weak CE city, should never do that. Cities like that need help from outside just like they need their HR troops built for them.
Rule 5 Growing cottages is more important than building gold and science improvements.
This is highly dubious and needs to be substantiated. There can be many situations where this is not true. What about other forms of infrastucture such as health and happiness some of which have economic multipliers? The courthouse have already been mentioned, but what of a forge (+25% hammers and upto +3 happiness) and a market (upto +4 happiness as well as the +25% gold multiplier).
It really depends on the production strength of the CE city (including the food surplus). It also depends on how close key techs like Printing Press and Liberalism are and how advanced the cottages are, villages and towns are different from cottages and hamlets. It depends on how reliant the city is on HR for happiness. The switch to US can be truamatic if no happiness infrastructure has been build. That depends on the availabilty of resources and the ability to trade for more.
Clearly cottages should not be whipped away unnecessarily. But at the same time every hammer invested in infrastructure (that will eventually built anyway) before US is available will save 3 gold and without gold multipliers that is 3 commerce. A whipped university (perhaps to meet the Oxford requirement) might slow down cottage growth but will immediately boost beaker output by +25% and is saving 600 gold in the long term. It is debateable whether that actually loses commerce due to lost cottage turns.
Rule 6: Plains should be ignored until Scientific Method.
The reason is that specialists are more valuable than plains cottages in the early game.
This makes little sense and requires clarification. To advocate running specialists in a city with low hammers and a low food surplus is very strange. If specialists are so useful it is easy to found a junk city dedicated to running 2 scientists, it only needs 2 grassland farms and a library. Wasting the food surplus of a valuable CE city on making GPPs is against the principle of city specialisation. A good CE city consists of developed towns and all necessary infrastructure. Anything which slows down the processes of developing the cottages or which slows down the building of the infrastructure is a bad thing and detracts from the main purpose of a CE city which can be summarised as "to maximise its beaker and gold outputs over time".
Here is a brief illustration of what might occur. Assume we have a city with 10 cottages and a library and a food surplus of 4, so 2 scientists can be run. Due to competition with other cities, in 100 turns this city can produce 600 GPPs, enough to produce the 6th GP. That consumes 400 food. That food if used to whip in infrastructure would translate into 600 base hammers, with OR and if some hammers became a forge that could be maybe 800 hammers of infrastructure where forge(120), university(200), market(150), grocer(150) might be some of those. How much stronger would the city be if it used the food that way? I just don't buy that part of the "run a few specialists argument" - if they are that good run them somewhere else. This is absolutely the last place specialists should be run. A possible exception might be if the CE city was lucky enough to have a food surplus of 10 or more (that level of surplus is difficult to handle with one whip per 10 turns) then specialists combined with whipping infrastructure would be a good way to manage the city, whipping away some specialists and then regrowing and still running some specialists, while all the time working all cottages. However if hills were available it would be better to use the food to work those instead of specialists.
Pre Biology Plains: why can't they be worked as farms after Civil Service allows chain irrigation? As long as they don't require extra health and happiness then growing the city bigger while working plains farms can be combined with whipping. The food surplus is thereby turned into hammers through Slavery and instead of wasting food running specialists the food is entirely used for growth and hence turned into infrastructure. Each citizen working a plains farm is food neutral and gives 1 hammer while waiting to be whipped. It is ideal whip fodder.
Take another example of where working plains makes perfect sense. A mediocre city with a 4 food resource, 6 grasslands and 6 plains. According to the rules this is not a good CE city, yet it is possible to have 10 cottages and 2 farms running at zero food but producing 7 hammers and with OR and a forge these are worth 11 hammers. If more hammers are desired then replacing a cottage with a farm will add about 2 hammers per turn with occassional whipping taking account of OR and forge multipliers. It doesn't really matter which tiles are farms and which are cottages and a mixture of grassland farms and cottages with plains farms and cottages allows some flexibility in regrowth during whipping.