That is where I built my custom “boot port.” Digging through my crap, I found an old micro headphone jack (I think it was a 3/32” mono input jack like they have on cellphones nowadays).
I had to crack open the Mini to do the RAM upgrade, so I used that opportunity to unscrew the CD-ROM and hard drive assembly from the motherboard. Inside, I ran two wires from the modem hole area to the boot button area. Thanks to MP3Car.com for providing me with the tiny y-cable. This Y-cable goes between the built-in boot button and the motherboard, and provides a second set of wire leads, allowing you to add a second boot button to the Mac Mini. I soldered the wires to the Boot Port, then used JB-Weld to mount the boot port jack in the modem hole. Now I have a semi-permanent boot port in the back of the mini that can plug and unplug with the rest of the cables seamlessly.
The goal of a dock is simultaneous plugging and unplugging of all the connections. This means all the connectors need to be firmly and precisely mounted in relation to one another. The solution was to cover the Mini in six-mil plastic; razor-out the plastic covering the ports; plug the cables into the ports; and then fiberglass over the wad of cables to hold them in position. The plastic protects the Mini from bonding to the fiberglass. The cables just bond to each other and become a pluggable wad.