hmmm, i'd like to see a little more than that if i'm honest. if i recall, 12V is for the audio amps, and RS232 stuff - plus feeds for drives.
it shouldn't cause any major stability issues, as most of the Amiga is hanging off of the 5Volt lines. Just if your minus 12volt's isn't up to scratch, your audio will definitely sound bad.
personally i swapped out my PSU to something more ATX-like years ago. i don't think i even have the original guts of my old A4k PSU around anymore. However, i did have to go up to somehing like a 550W SFX psu to get the equivilent juice on the 5volt line, as most PC PSU's are focused on 12Volts - for the mainboard and PCIe accessories - with the power regulation for the CPU and stuff being done on the PC's board itself. My A4k's already eaten a "250W" flex-ATX PSU as it couldn't cope with what the A4k needed for juice on 5volts.
http://www.ianstedman.co.uk/Amiga/amiga_hacks/Amiga_Power_supplies/amiga_power_supplies.html#wiringa4000
