Chris,
I use my original 2 window topper that I bought for a Beach a few years ago. It’s since been used on my Ocean both with and without VW roof bars.
I don’t know if the Beach and Ocean roofs are different heights, but I have found that when using it on the Ocean it has a couple of inch gap at the bottom, which for me has improved the ventilation. Likewise, when using it with the roof bars, the gap is larger. The bungees still work and again the ventilation seems better.
So back to your questions, for me windows (and I have just bought a Kamper Cosi because I thought 3 windows are better than 2) and you can probably still use a normal topper even if you do have bars. For me, this would only change if I ever got solar panels.
Cheers
Steve