Yer not entirely wrong...but that's a different pitch you're referring to.
Most tracks these days are a 2.52 pitch...and that's definitey a spacing thing with how it meets the drive sprockets. There's all kinds of different pitches you can buy, but if you want to change THAT pitch, you have to change drivers on the front axle or they won't mate with the cogs and/or windows of the track properly.
But that has nothing to do with a '6 pitch' track lug pattern.
As for your cutting windows question: Some leave it clipped every third and leave the closed windows in place (stock on many tracks), some have it clipped every third and put SLP pads in the closed windows, some cut the windows out and leave it clipped every third (stock on a few tracks), some cut the windows out and add the extra clips to every cog making it "fully clipped" (stock on many tracks). Everyone has their own opinions on how these different configurations impact hyfax wear and speed, and that debate will never end....
You can add or remove clips to/from any track with the right tools (or even with the wrong tools!), and many here do such things themselves all the time.