Can you blank the tubes in software? If so you could implement dimming in 
software, which is all PWM is. No need for a dedicated pin. I did this for an 
Arduino controlled clock kit I bought. There were no timers left, so I just 
kept track of whether the tubes should be on or off in the 'PWM' cycle in a 
small PWM class. Essentially your 'clock cycle' is however fast you can get 
around your main loop.

I implemented cross fading the same way!

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