I have used pistons both ways, for various reasons (the upside down one, the way that the website promotes as "stable" was actually an accident), and I can say that regardless of orientation, I have never had any problems with pistons.

Whether the bulkhead is toward or away from the charge or somewhere in the middle, I don't think matters nearly as much as 1) the skirt is long enough to preclude any significant twisting and 2) keep the tube and skirt reasonably clean. Some lubricant might also help, although I have not tried any yet. Plausible suggestions I have geard are baby powder, dry soap and maybe graphite powder.

For my L3, I'm using a piston in the upper dual deployment section, with an option to use a second one in the section above the booster. The other alternative for the booster is the zipperless, blow-the-section-off-the-booster-exposing-the-harness-attachment method. Either way, I feel safe... though I haven't ground tested yet. That'll be a blast... literally. The rocket sims from 8k to just under 19k depending on the flight configuration and/or motor (obviously). I'll try putting the piston in both ways, and let you know which way appears more reliable. Never used pistons before, so this will be fun. 8)