You can point to articles all you want, and suspect whatever you want. Real world experience is, if I accidentally boot into the built-in 80 GB 5,4000 rpm drive, the mini is excruciatingly slow in comparison with the 320 GB 7,200 rpm external drive connected via Firewire 400.
Boot time is meaningless. You need to run a diagnostic tool to assess your drives' performances. Here's the Intech Quickbench result of comparing my Mini's internal 60 gig 5400 8 mb cache Segate SATA drive vs. my external Seagate FW400 500 gig 7200 rpm 16 mb cache drive:
Internal 60 gig SATA drive
Extended Test Size: 2 MB Read: 6.308 MB/sec Write: 121.974 MB/sec
Extended Test Size: 3 MB Read: 24.096 MB/sec Write: 121.369 MB/sec
Extended Test Size: 4 MB Read: 24.189 MB/sec Write: 110.763 MB/sec
Extended Test Size: 5 MB Read: 23.575 MB/sec Write: 75.529 MB/sec
Extended Test Size: 6 MB Read: 25.667 MB/sec Write: 64.713 MB/sec
Extended Test Size: 7 MB Read: 25.979 MB/sec Write: 60.063 MB/sec
Extended Test Size: 8 MB Read: 27.472 MB/sec Write: 52.914 MB/sec
Extended Test Size: 9 MB Read: 29.222 MB/sec Write: 52.506 MB/sec
Extended Test Size: 10 MB Read: 29.181 MB/sec Write: 49.032 MB/sec
FW400 Drive
Extended Test Size: 2 MB Read: 25.791 MB/sec Write: 21.071 MB/sec
Extended Test Size: 3 MB Read: 16.029 MB/sec Write: 30.791 MB/sec
Extended Test Size: 4 MB Read: 17.705 MB/sec Write: 30.752 MB/sec
Extended Test Size: 5 MB Read: 20.273 MB/sec Write: 31.485 MB/sec
Extended Test Size: 6 MB Read: 16.750 MB/sec Write: 16.146 MB/sec
Extended Test Size: 7 MB Read: 29.418 MB/sec Write: 27.981 MB/sec
Extended Test Size: 8 MB Read: 24.208 MB/sec Write: 19.158 MB/sec
Extended Test Size: 9 MB Read: 30.167 MB/sec Write: 27.574 MB/sec
Extended Test Size: 10 MB Read: 26.503 MB/sec Write: 31.025 MB/sec
Clearly, the better performance is from the internal 5400 rpm drive with its 1.5 gbps SATA interface vs. the 400 mbps FW drive. Your FW connection is a bottleneck - your drive is only as fast as the FW controller. If you want to make your Mini perform better, put in a 320 gig 5400 notebook hard drive. They're only about $140.