This HRTIM is also mentioned in this thread but it comes with a lot of constraints, and is not a true high speed clock, but something with delay lines,
Yeah, but on the other hand this specific case would be exactly what the designers had in mind: high resolution PWM, so I would expect this is a very easy job with STM32F334 or the friends. Just be careful that some values close to min and max duty are illegal, in other words you can't output 1/65536 with HRTIM but you can output 16, 17, or 18/65536 just fine.
Then again, I also question the idea that 16bit accuracy on PWM is needed and then frame-by-frame variation depending on how the shutter and PWM happen to coincide is 1/50 or roughly 6 bits.
PWM is probably inaccurate anyway, what are you going to do with the PWM, control the LEDs from a voltage source using some MOSFET? Then the brighness will vary based on voltage and temperature variations. Constant current circuit is really needed, and then you could just adjust that current setpoint.
If both accurate amount of photons with short exposure (i.e., uniformity of light), and quick setpoint changes are needed, then maybe design two filtered constant current drivers and a quick switch between them. You can basically short-circuit the unused constant current driver while the other is connected to LEDs.