Nitrous burns much hotter, so coated pistons become mandatory for constant usage if you're running a 150 shot+, which is also rod slinging territory, as you'll be throwing down about 500 ft-lb of torque at the wheels. The occasional pass won't hurt anything with a 100 shot or less, as the pistons have time to cool to normal temperatures, especially since the 4.6 doesn't use cheap alloy or aluminum pistons. My quarrel with NOS is having to refill the bottle at $40+ a pop.
Injectors and intercoolers are very simple modifications that are included in the bulk of SC kits. If you're looking at a full top end build, something as simple as injectors and an intercooler is like comparing stitches to brain surgery. As long as you're in safe power ranges, you won't blow your internals. There's a reason Ford put Roush and Saleen blowers on stock 2005-2010 GTs.
As an engineer, I don't understand any of your reasoning for choosing N/A over FI on those grounds, as FI only makes the engine run more efficiently. You only run into problems when you try to push things way too far, just like if you run a Stage 3 cam and throw a lifter.
But it's your car and your opinion, so it's ultimately your decision. I look forward to seeing your build with whatever route you choose. I'd suggest PMing stlwagon, as he built his GT N/A for road racing with over 400rwhp.
2007 Mustang GT 5-speed 3.31 gears, Hidden Hitch Receiver, Barton Short Throw, JBA LTs, Borla Touring Axle Back, and Lito tuned SCT X4. BMR SP009, KYB Shocks & Struts, J&M CC plates, J&M LCAs. 4 Piston Brembos
255/45ZR18 front 295/40ZR18 rear
Department of Boost GT450 with 2011 GT500 M122, TB, & CAI | 13/14 GT500 HE & IWP | GT500 dual pumps | FRPP 52lb | CMS Stage 2 Blower Cams | Comp Springs & Retainers | AEM boost & wideband | 8 rib conversion | Track Spec GT500 Vents