Why is this the case and what does this mean for me?
It is because the servo library uses the internal timer that is used to generate PWM signals on those two pins.
It is important if you want to use PWM in addition to using servos.
So I can't use those two pins for any servos if I have more than 11?
No that is not what it said. Servos are not PWM.
Can I just use any of the digital pins to connect to those 48 servos
Yes.
Be aware that servos take a lot of current and generate a lot of interference so you will need a good external supply with good supply decoupling.