Never heard of any of those ways, but then again, I've never used imperial measurements.
On a roadbike you should aim to have around 3cm standover clearance, but that's only for safety, so you can comfortably stand at the traffic lights, etc.
For calculating frame size and seat height, I like the simple Greg Lemond formulas:
a. Your centre-to-centre seat tube will equal (inseam x 0.65).
b. Your centre-to-top seat tube will equal (inseam x 0.67).
c. Your bb-saddle height will equal (inseam x 0.883).
There is also a rather detailed calculator available online at Competitive Cyclist
. There are lots of explanations too. However, I find that the Eddy fit and the French fit given on this website are too big for me.
All this is for proper traditional frames though. Modern "compact" frames are designed to get everyone to fit on just 4 frame sizes. It's a way of cutting costs for the manufacturers. The seat height calculations are still good, but the rest of the calculations are a waste of time if you intend to ride a compact frame.