For my set up and the tools I have available, I find that slotting the fretboard while it is still square works well. You do have to be careful when you do "cut" the fingerboard down to the final size that you avoid tear-out. All those fret kerfs present a lot of chances for tear-out.
I cut my fingerboard oversized, leaving it square. I then radius the board followed by cutting the kerfs (using a table saw and the thin-kerfed blade).