Im running an Apexi power FC on my Civic and its mapped "properly" in fact its mapped very well.
Care to explain rs250nut ? as i think your talking **** !
Only reason i went for the Apexi is the fact you can pick them up for a few hundred quid new now for the Hondas, does everything i need it to do, if you want launch control, datlogging etc. then go for something else but for the money its a decent bit of kit, just look at how much theses cost for other cars there in the region of £600 up and the fact is the Apexi power FC was designed and made for the Mazda RX7 hence FC.
As for the original question yes this will work with boost but i wouldn't recommend using the Power FC's boost function AS I HAVE HEARD ITS NOT ALL THAT GREAT SO GO FOR A STANDALONE BOOST CONTROLLER AND HAVE YOUR MAPPER SET IT UP AND MAP IT.