Keep in mind that in general the BOMs are made to be compatible with the NatSemi eval boards. Thus surface mount parts because most of their eval boards are surface mount. (I think in the case of active filters that they don't actually sell eval boards...)
It was never intended to be a general-purpose simulator! It does some very generic and common topologies and nothing else, and that's what it's supposed to do (in addition to selling more NatSemi chips!)
Complaining about it is like complaining that you bought a "one-size-fits-all" pair of pants but the seams split after only 4 people :-)
Tim.