If the only reason you are cutting upside down is to allow for the dust collection, than why bother? Jigsaw's are the least "dust-throwing" tools and are not used as much as sanders/routers/cic saws, so just use it the right way and sweep up afterwords.
I'm no Festool hater, I've got the CT, the TS, Domino, rotex, Of, etc. etc., but I had and sold the jigsaws because they didn't offer one significant advantage over the bosch and in fact have a couple disadvantages. The first being the blade guards mentionede above and also, they are louder than the Bosch.
The only upside down jigsaw cutting I'd want to do is when coping trim. Otherwise, right-side up seems the smartest approach.
Julian