Boost readings

It could be me being me -overthinking- but I read that the boost guage reads the maifold pressure, not the turbo outlet pressure, and if that's so, assuming that a stock 86 GN runs at 12#, wouldn't the boost gauge read 8#(approx., due to intercooler loss) or, does it run at 12# at the manifold, or does our boost gauge actually read the turbo outlet pressure? I am asking this becasue I believe I have a Red Armstrong 93 octane chip(another post), which runs at 17#(stated), but my boost gauge only reads 11 or 12#s. Or, is it that my boost regulator(the stock, non ajustable one right now until I have time to get adjustable one mounted) has fizzled out?