[Colt Delta Elite]

I was thinking of overall layout. For instance, placing the master bedroom between the likely entry points and the other bedrooms; channeling intruders into routes favorable to the defender, exit points, etc..

I'm looking for something that doesn't scream "Paranoid Gunner Lives Here"

Too late.
Get real. You should be concerned with building wider doorways and installing ramps, as you have a greater likelihood of being disabled than having a home invasion.
Do you drive a Volvo too?

tcc556guy: maybe even to the point of sheetrocking a long gun behind a specific wall so that in an emergency the homeowner only has to smash the sheetrock to get at it

probably should back that up with dropping a few handguns into the forms as they pour the slab!