A longer neck is more flexible (which isn't a good thing in a bass guitar - scale length isn't responsible for the issue of flabby B strings. For some reason, string makers seem to like an arithmetic progression of diameters - 40.60, 80, 100, 120. This doesn't really work - the tensions vary too much, even in a 4 string set. In a 5 string set, the situation is just worse, and the place that suffers most is the B string
To get equal tension across strings on a bass, the diameters need to be 4/3 in ratio (which is also the frequency ratio - there's a square and a square root in the Physics equations, which thankfully cancel each other out). String makers don't seem to be hip to this - if your E string is good tension wise at a diameter of .100, your E should be a .133 - so nominally, a .135 would be good.
I like low tension strings. The sets I just ordered (had to order singles to do this) are 40/52/70/95/130. That's a well balanced set, but the fact that an E string that's skinnier than most sets and a B string that's bigger than most sets are what it takes for equal tension just hows you how far off most sets are.
Low B string tension isn't a scale issue - it's a string issue. If your E is .100, try a .135 B. If your E is .105, try a .140 B