The timer hardware in even the most basic Arduinos is extremely capable. Pretty much anything you can think of has been designed into the hardware. But getting to that capability is difficult. The datasheet does have all the information but not in a form that can easily be written into an Arduino program.
My interpretation of what you need is two PWM signals, which are synchronized. You only want to drive each one of them in the 0-50% range and you want them synchronized so that when they're both at 50% they don't overlap. You may, for example drive one at 25% and the other at 50% but they always stay locked in frequency so that they're never both on at the same time.
I'm sure this is possible with at least some of the Arduino variants. Personally, I don't believe it's worth the time digging into the datasheet. Just set up a timer ISR and drive the pins "manually" in your code.
I'm still not clear on the requirement. You're driving vibrators which presumably resonate at 50Hz, at least the mechanical resonance is around that frequency. Electrically, they're probably big coils of wire with a big inductance, giving an electrical resonance. To drive these efficiently (without burning the coil or the driver) you need to know what that resonance is. You seem to be ignoring the "off" half of your drive signal. That is just as important as "on". I would expect to drive them with a full sine wave which goes positive and negative. A modified sine wave or trapezoid may be useful, depending on the drive electronics you have.