Uhm, it can be used, i think, but you really don't need a pwm for that, just a flyback with an oscillator, cause, after all, the high voltage unit, don't control anything, is just a power supply (btw, i have a plasma ball that use just a 4007 as oscillator and a TIP120 as power stage, for a flyback transformer ..... cheap, but works
)
I mean, no reason for complicate your life ..... just try a schematic that can give you a decent DC output for the resonant cavity, and you're ok.
Also, for turn it DC, you need high voltage capacitors and diodes (usually 10 KV ones) ..... not cheap.
Oh, just as my usual DIY maniac side, i remembered, there are some very good high voltage units inside the old photocopiers, the big old ones have the better ones (are used in the transfer process, for charge the paper and he drum surface, and transfer the toner powder from one to the other via electrostatic charge)
In the past, i recovered some 5600 V and 9800 V units, from some old xerox and canon, and these units usually are ready-to-work ..... mean, a box or a circuit that have already all on, flyback, oscillator, driver, you just need to power up it ..... and if you can find some of these things from some scrap deposit, usually they come for free
Just as idea.