I went with the 20-39, because while the 16-46 has lower extension, the 20-39 provides more SPL's. Add in the fact that the room will likely add extension down to 18 Hz or less, and I felt that I was sacrificing very little in the extension area while ensuring plenty of punch.
Real world experience however, now that I've had the 20-39 for a while, is that the SPL output is so overwhelming that I rarely have the power output beyond 30%. Do understand, I am a bass-o-holic and at this level can bring the neighbors a-knocking on my door. Thus, I have to believe that the 16-46 would provide more than enough SPL's, while giving that extra visceral impact.
Given the chance, I would now go for the 16-46. My space is 2100 cf, BTW.