I use shift-registers to control the individual driver-transistors in non-multiplexed mode. Then, I tie the shift registers into a serial chain so it uses only 2 pins on the controller (clock, data). So far I've used FPGA's for control, but I'm switching to a RasPi for the next project. Some shift-registers have output-enable pins, so you could use that for PWM, rather than trying to serially shift-in a PWM pattern.
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