What real difference does the lsa on a cam make?

Absolutely. I agree 100%. I am only saying what I have seen and done. There are so many variables there's no way to nail it down.
Yup. I've read their stuff. However the quoted section leaves out (probably purposely due to the confusion it can create) the affects of stroke, rod angle, crank position, port flow, and port balance on potential overlap and lobe placement. Wallace does touch on some of it in the next paragraph:

"
Overlap and Compression- A very common idea, although for the most part incorrect, is that overlap bleeds off compression. Overlap, by itself, does not bleed off compression. Overlap is the angle between the exhaust closing and intake opening and is used to tune the exhaust's ability draw in additional intake charge as well as tuning idle vacuum and controlling power band width. Cylinder pressure is generated during the compression cycle, after the intake valve has closed and before the exhaust opens. Within practical limits, an early intake closing and late exhaust opening will maintain the highest cylinder pressure. By narrowing the Lobe Seperation Angle 'LSA' for a given lobe duration, the overlap increases, but the cylinder pressure can be increased as well. Thus cylinder pressure/compression can actually increase in this scenario, by the earlier intake closing and later exhaust opening. By increasing duration for a given LSA, the overlap will increase, the intake closing will be delayed, and the exhaust opening will occur earlier. This will decrease cylinder pressure, but the decrease/bleed-off of compression is not due to the overlap, it is due to the intake closing and exhaust opening events. "


Wallace is speaking strictly in terms of the camshaft. Which to me is overly generalized for something so critical but I can understand why they'd stay simple as the website is meant as a quick reference guide. And a good one to boot.
My own opinion is if someone is interested enough to ask about it I'd rather consider and talk about it as more of a "case by case" type thing rather than being too general. Leaving things too general leaves the hobbyist/enthusiast/reader a strong potential for those statements to be considered a specific "rule". Because the cam is dependent on the other parts, IMO there is no hard fast rule unless you remove variables to simplify the choices. That's why I said talk to the grinder. They should be less general and the recommendation should reflect a more complete selection of "inputs".