I forget that not everyone uses Audyssey Dynamic EQ for bass EQ.
So for Pioneer, Yamaha, Sony, HK, Onkyo, I don't know which way I would prefer.
But for Denon/Marantz w/ Audyssey Dynamic EQ, I unequivocally prefer to connect the Sub Output from AVR to Tower LFE Input and let Audyssey DEQ EQ the subwoofer.
Otherwise, the Bass on the towers would not be equalized by Audyssey Dynamic EQ.
When I had Revel Salon2 and B&W 802 Diamond, Audyssey DEQ did absolutely nothing for the bass.