It could be due to the fact that ... the Fast Track Ultra ... is optimized for 96/24, whereas another audio interface may work better at a lower sample rate.
Dan Lavry has said as much. An interface designer has to pick a sample rate to design around, and might well choose 96KHz as that optimal rate. I would have expected a prosumer-class device like the Fast Track Ultra, being targeted at hobbyists, would have been optimized for 44.1. But who knows what their reasoning was?
And of course you do get lower latency with higher sample rates, whether it sounds better or not. For me, 5ms is fine. It's no different than being 5 feet away from your amp or monitor on stage. I don't play soft synths in real time, as I prefer hardware synths for tracking and then substituting computer-based samples later on. Latency is therefore never an issue.
But mainly, 44.1 makes sense for me because I use a lot of synthesizers. Whether soft or hard, they are all playing 44.1k or 48k samples. There is no benefit to upsampling them, so I'd just be burning up disk space for nothing.