Usually these supports are very big and inhomogeneous in terms of distributions of active particles, so, how could be measured the specific MSA (m^2/g active phase, ex platinum)?
The principle to measure the SSA of active components is to measure the amount a reactive gas can adsorb chemically on them. The reactive gas can be hydrogen in the case of metals. Sorry I do not have references in hand.
You can measure surface area of material surface with complex surface topography by using optical profilometry (ex. WYCO NT series) as surface area developed (Sdr). But, your surface should have no undercuts in surface structure.
No, WYKO system will automatically estimate flat surface as guide area for the measuring surface area deleloped. Thus, you don't need to make flat surface. Your micro-rough surface is OK for the measurement.