Raised port heads are really geared towards the high horsepower crowd. Trickflow R-Series heads do require a non-standard header flange.
There are so many good aftermarket heads out there that the trouble of going to raised ports is hardly worth it. Ford, Roush, AFR, Trickflow, Canfield, Holley and Edelbrock all have heads that will support upwards of 450hp+ , all having standard exhaust flanges.
Most GT40 headers are custom so I guess this isn't a problem.