Hi Guys
A flourocarbon protector works by coating the carpet fibres with a thin film , which is both oil resistant and also alters the surface tension so that water based spillages do not wet out and can be soaked up.
In practice it is difficult to get the polymer particles to form a good film , and this is one reason why solvent based protectors are better, as the poymer can be dissolved rather than suspended and will therefore form a better film on evaporation of the solvent.
Solvent based protectors would be too expensive and have too many H&S problems to be generally used on carpets.
The water based flourocarbons will be small particles of flourocarbon suspended in an emulsion. The chemists who developed them will have tested the optimum pH for film formation and this would appear to be about 6, hence the need to use an acid rinse/prespray.
It's worth bearing in mind that if you clean with a lower pH solution then this will be easier to neutralise, remember pH is logarithmic so aPh 10 is ten times more alkaline than pH 9.
As for putting the protector in the solution tank, the biggest draw back is that you would remove most of your expensive protector and put it down the drain.
Cheers
Doug