Another difference 'might' be Audyssey MultiEQ XT Pro. I just emailed Chris K from Audyssey about this yesterday - his reply was "Onkyo has not informed us that the 5507 will be installer ready. As of today there is no Pro software available for it from Audyssey. Please contact Onkyo directly to ask them about their plans.
Onkyo indicates on their own website that the 5507 is Audyssey "MultEQ Pro Ready".
I spoke with the famous "Axxx" who most people seem to be buying their 80.1s from on AVSForum's 80.1 thread and he indicated to me that he sells both the 80.1 and the 5507 and verifies that the two pre-pros are equivalent with the exception of the minor differences already mentioned on this thread. In addition, the 80.1 comes with Integra's 6-month exchange feature (if problems occur within the first 6-months, the dealer will swap it out for a new one). This feature is not available for the 5507 and should the unit have problems, you will have to go through standard warranty procedures for repair rather than replacement.
As for the reliability of these units, "Axxx" went on to indicate that both the 5507 and 80.1 have been reliable so far (Axxx owns an AV store in Texas and has also been an authorized Onkyo service center for 20 yrs). With Onkyo/Integra's previous pre-pros (as recently as the Integra 9.9), he would sometimes see these units come back for repair because of damage to the internal cards or power supply from shipping/mishandling but that with both the 80.1 and 5507, Onkyo has placed foam insulators to separate the cards and power supply from other components and so far he has not seen any of the problems that have plagued the previous units.
As for the minor difference in weight between these 2 units, this is due to the metal door on the faceplate of the 5507 that's used to cover some of the lesser used connections and the removable rackmounts. The 5507 is also a bit deeper by 8.5mm because of this protruding metal faceplate. Interestingly, because the 5507 has more metal (faceplate and removable rackmounts), the 5507 lists for $50 more than the 80.1 although street prices for the 5507 are generally less than the 80.1.
When I asked "Axxx" why Onkyo would make 2 identical pre-pros, he stated that their Integra line is geared for the high-end consumer market while the Onkyo Pro line is targeted for professional musicians/studios although why musicians/studios would need a 9.2 channel AV pre-pro was beyond his understanding.