Export from STP with the levels that you want on playback from the system. If you want peak level at -12db, that's what to export.
The -31 comes into play when you are building the DVD. There is a setting in the audio tab of the ac3 DVD preset in Compressor where you can specifiy the Dialog Normalization level. -31dbFS will pass the levels you set in FCP on through to the DVD.
I don't deal with Blu-Ray, so can offer no advice there.
Thanks for the reply. I'm exporting the AC3 directly from STP.
My confusion is why the STP manual says "if the dialogue in your project averages around -12 dB on the level meter, enter -12 in the Dialog Normalization field." then says "If you enter -31 dBFS (in the Dialog Normalization field), the attenuation is 0 dB (31 dBFS–31 dBFS), and the source audio levels are not affected at all."