G'day Justin - looking at your tuning options, I think the mods that have been applied to the MPS have been done as the best way of achieving results in the absence of a flash tuning option. Flash tune options such as Cobb AP and Versatune eliminate the need for some of the items you've mentioned such as the boost controller and piggy backed ECU.
Presently I can't see Mazda MPV listed as supported by Cobbor Versatune, however Versatune does support the CX-7 and it may be worth appealing to Versatune for support.
Provided it tests healthy on compression and leakdown and you are happy to learn the ins and outs of the bespoke tuning solution that's been applied, it might be a good option for you.
"Blue Meanie" 2007 Aurora Blue MPS 3 - 18x8.5+44 SSR GTX01 - 235/40R18 Michelin PS5 - 3.5" ETS TMIC - CPE stg 2 mount - HKS/CPE BPV - 2XS inlet - 2XS short shift - Corksport turbo manifold - HT 98 octane tune - Leather/Aluminium handbrake - Momo shifty knob - 7" touchscreen - JDM Mazda Retractable dashtop screen assembly - Bespoke Raspberry Pi Android based GPS/Carplay and instrumentation - 36AH reserve battery and C-TEK isolator - TEIN Street Advanced coilovers 1" drop - Superpro bushings - 220Kw/410Nm.
"Lipstick" 2013 Velocity Red MPS 3 - 18x7.5+48 Enkei RPF1 -225/40R18 Federal RS-RR - CPE TMIC - COBB inlet - CPE stg 2 mount - COBB Stage 1 98 octane tune - COBB shifty knob - 2XS short shift - 2XS turbo manifold.