The discontinuation of pack rat supprised me too! Just four years of production!
The main issues with the Pack Rat (IMO) were the brakes and the forks, two issues not mutually exclusive. Tire clearance also came into play.
The world was very ready for a "budget" (more accurately a readily available) randonneur with disc brakes and a threadless steerer a la the Elephant NFE (the SOMA Grand Randonneur is threaded with a quill stem). But those bikes have true low trail geometry, and the NFE did have issues with its fork and disc brakes in the past, as low trail forks and disc brakes traditionally haven't played well together. The NFE problem is in the past, though, and I'm not casting aspersions on it. Jan Heine never issued a Grant Petersen style Fatwah against disc brakes, but he's never been a fan of them on 650B traditional randonneurs, and he has an influential voice in the community that ride them. He
did ride a tandem with Lili Herse that her father had made, so that influence is not exactly unwarranted. Still, traditional randonneurs, with light, springy forks made of really thin tubing, could not handle the stress of disc brakes acting on the crown of the fork, and so rim brakes were the default for randonneurs.
All that said, the PR naver had true low trail geometry, and as such, should have been able to easily accommodate disc brakes, with those Natch mid trail forks, and yet mounts were not provided for them. There was some Surly press release at the time speaking about how they felt it handled better with a front load with its mid trail forks, and yeah, great. But I feel they badly misjudged the segment of bike buyers would would have bought the PR by not giving it low trail forks (the rim brakes would have made a certain amount of sense with low trail) OR by giving it disc brakes (the mid trail forks would have made a certain amount of sense with the forces of disc brakes). With mid trail forks and rim brakes, though, the bike didn't make a lot of sense to the people that would buy it.
The other thing is tire width. The PR had clearance for 650x48B, which is perfect for WTB Horizons and Byways. That said, IMO, it's not enough. In the US, their primary market, traditional randonneurs are probably most popular in the Pacific NW, home of The Jan (he of "Welcome to the Industry Reen Hers" bicycle pubes fame). Up there it's rainy, and rough in parts, so full fenders with chunky MTB tires is where things are at. The ability to run 700x40C and 27.5 x 2.1 with heavy tread for mud, would have made the PR a much more attractive proposition for the market it would have sold to.
The Pack Rat, with the tire clearance of the Midnight Special, true low trail geometry and disc brakes would have been a serious alternative to the Soma Grand Randonneur and the Elephant NFE. As it was, in my opinion, the Pack Rat just didn't make sense as it was, the segment of bike buyers who understand and would buy a traditional randonneur understood that and thus the bike's sales suffered. As someone in the forum said "they must have sold dozens of them."