There's another good reason, but also a caveat from my experience.
The good reason is that USB mass storage is nice and easy in the logic board BIOS and you can switch off any SATA channels that may or may not support AHCI and may or may not consume power. If you like Macs but run all your dedicated miners on Linux (like me) then you don't need the additional confusion of AHCI vs IDE etc.
The caveat is that if you run the Phoenix miner, and have multiple dedicated GPUs, you're likely to be running multiple instances of Phoenix, sending the output of the program to a logfile. I don't know whether this has been fixed AT LONG LAST yet... but if you leave Phoenix running for a day redirecting stdout to a logfile, you will end up with 100 MB of logs. Leave a few weeks on a flash-drive based Linux system and you may end up running out of space. The constant writing to the device also trashes the poor wear-levelling on cheap flash drives. They're not SSDs, don't treat them like such - it's actually a great idea to consider using a different filesystem (like btrfs or at least anything that doesn't run journals) if you're installing a 'normal' Linux distro install onto a flashdrive.
I've broken an 8GB flashdrive stick from running Linux on it, using standard Ubuntu filesystem settings and a phoenix miner setup that wrote to logfiles and then created / deleted short versions every 3 seconds... flashdrives are NOT good for LOADS of I/O....
A +1 for cgminer then. It supports custom logging intervals. I set it to 2 minutes which is enough granularity while keeping logs small.