These rules were meant to be a quick and dirty way for retail workers to fit you (i.e. people who do not have a sound knowledge of fitting trying to sell you a bike in a short time). Do not follow blindly.

saddle nose to stem - What does your forearm have to do with the way the bike fits overall? I fall 2 cm short of my bars on all my bikes and have pretty short forearms.

handlebar obscuring axle - This rule never made sense to me. The more your drop your bars, the longer the stem you will need to obscure the bar. When you raise your bars, you need a shorter stem to obscure it. In reality, you generally want it the other way around: longer stem with higher bars and shorter stems with more drop. Your viewpoint also changes depending on where you ride. Your eyes are in different places dependent on whether you ride on the hoods or the tops. This also ignores the fact that bar reach varies a lot between different bars. What I think is important is getting the center of your hoods, at the least, in line with your hub to get the best handling out of a road bike since road bikes need more front weight. That said, my handlebars do not obscure my axle.

What I suggest is using a goniometer while you are on a trainer to measure body angles. They are cheap. Then compare them to this site: http://bikedynamics.co.uk/guidelines.htm. I do this on all of my bikes and have done it for a few friends. It works pretty well, but is also not meant to be followed exactly. It is, at the least, much better than silly guidelines like these and KOPS. Get roughly in the region and then make micro adjustments from there. Once you have something that feels really good, write down your actual body angles (some goniometers are more accurate than others) and the geo of your bike for future reference.