I don't have the Winnebago top, mine's a Weekender.? But I installed the tracks on my poptop and I think that they put less stress on the top (maybe even reinforce it) and also allow you to adjust the bars as needed.
GoWesty uses the track approach for their Winnebago roof rack kit, so they must work.? ?They have very helpful installation instructions.? So that's what I would do if I had a Winne.