The drop basket might require the rack to raise 1/2" at most, compared to without it. In most setups the middle set of towers are as low as they can go, which provides about a 1" gap between the cross bar and roof in the center... agreed with @Mike NXP that if it were any lower it would be less useful. But that drop basket only hangs about 1" below the rack surface, so you set it up just high enough that it can't deflect & rattle against the roof. If you want the lowest setup possible then yes forgo the drop basket. You could also do the non-tapered Expo bar and that would allow the front to be maybe 1/2" lower also. Not going down a few inches though, every variant is about the same height, and in general within 1" of the factory cross bars.
As for the gussets I also rarely put a strap into them- they're more for quickfist clamps, so adding shovels, hi lift standards, etc. But on those occasions where I have a wide mattress or something it's nice to reach under and put the hook in the gusset. All other times I just wrap the strap around the bar then hook it to itself.