I guess you could use an opto, but not really necessary. I'm assuming you're going to have everything with a common ground, just without the fan's current return through your board. Given the small but real /trace/connection/wire resistance, you don't want the pulses of fan current to induce noise in your board's ground.
As for the circuit, a linear ramp sawtooth wave is easy to make with a 555 timer. Then run that into a comparator along with the output of your error amp (variable gain on that would be cool), voila PWM.
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