The effects of a long taxi vary, but generally increase brake temperatures. Brake use during taxi, and wheel temperature increase from the taxi process don't usually cool the gear.
In my operation, the result of a three mile taxi alone can put brake temps into the red.
Leaving the gear down after takeoff obviously isn't done to prevent taxiing or taking off with high brake temps. It's done when a prolonged taxi has left high temps and when the leg will be short. Likewise, early extention prior to arrival is a useful and often recommended technique for cooling brakes and gear before landing.
Brake temperature is not only a function of remaining stopping power. Clearly the amount energy the brakes can absorb and transform to thermal energy (heat) is limited, and therefore the capability of the brake has it's limit. However, simply because the brake gets hot doesn't mean it quits working. Carbon brakes improve in performance with an increase in temp, up to a point. Organic and semi-metalic experience a decrease in the coefficient of friction as temperature rises, again, up to a point. Each type of brake material has a temperature range at which it's most effective; increase the temp above that point and the brakes effectivess will "fade" or decrease. Extend a little beyond that, brake damage can occur.
It's not just the brake damage. High temperatures damage wheel assemblies and tires. Internally, tires gas at high temperatures, creating flammable mixtures inside the tire, which can explode. Rubber deteriorates in the presence of heat. Fuse plugs melt. Hydraulic fluid boils, drastically reducing it's ability to deliver uniform effective pressure.
A brake cooling chart gives you a guideline. Simply because the chart says an hour doesn't mean in an hour you can disregard the temp indicators and go fly. It means one can expect an hour for the brakes to cool. This can be decreased by the use of fans, or it may take longer. It's guideline.
which is correct option?
a) brakes off wait 35 mins before taxing.
b) wait til brakes cool to normal operating temp and then taxi.
c) ignore brake cool temps altogether.
Obviously one doesn't ignore brake temperatures. The cooling times are advisory, indicating what you can expect. Any limitations prescribed are just that; limitations.
You may have data describing what to anticipate for taxi, or you may not. You may be able to plan your cooling for the additional temp rise of a long taxi, or you may be taxiing at light weights with an engine shut down and have little brake use or temperature rise.
Wait the 35 minutes, monitoring temperatures and evaluate. Look for temperatures in an acceptable range for your aircraft and intended operation, then decide. If you happen to be using cooling fans, don't simply note the temperature and go. When the fans are removed, you may very well see a temperature increase as the temperature normalizes, or becomes more uniform again, throughout the brake and gear assembly.
Don't ignore those temperatures.