it's fine to have your feet resting on the pedals (as is written into the books in two airlines I've worked for).
What is written in the books in the two airlines you have worked for are nothing more than the personal gimmicks of whoever in management wrote the books. The law of Primacy ensures you remember what ever technique was taught to you in your early training. And if that includes riding the rudder pedals while the other pilot is handling, then fill your boots as they say.
One of the greatest potential dangers of that particular habit (riding the pedals in case you decide personally to apply brakes on for some reason) is the take off roll. Let's assume the captain is conducting the take off. The F/O is riding all primary flight controls except the thrust levers. After all, if you think that riding the brakes is a good flight safety precaution, then to be consistent you should also ride the control wheel as well.
Nearing V1, you see a flock birds rising from the runway ahead. You tense up. But the captain says nothing and instinctively or maybe inadvertently, you apply partial brake pressure in anticipation of the coming abort. But the captain has already decided to continue because he isn't worried about the birds. Your nervous tick in applying slight brake pressure then automatically dis-engages RTO. Now if a real abort takes place there is no RTO just when you need it most. The law of unintended consequences?