Hal, that's the formula I've always gone by...there's lots of different formulas out there. Some confusing, some not so. I always compute to cc's, since that's what most vol's are given in, except cyl. displacement. Cubic inches X 16.39 will give you cc's.
Yes, the valve reliefs and area above the ring can add a few cc's, and lower the compression. I always do a liquid pour with the piston in the cyl, which gives an actual exact dome volume. In most cases like yours, it's really not critical.
You could get a bigger dome, which means a heavier piston, or find smaller chamber heads.