Good article. And with better algebra.
You are correct, I never said modulating condensing boilers were not a good idea. We install them regularly with outdoor reset and customers save anywhere from 40% - 60% on evergy usage compared to the old cast iron on/off boilers. These savings come mostly from the low return water temps most of the year rather than the benefits of modulation.
I just don't like it when I hear: "It modulates so it doesn't matter if its oversized" Oversizing a mod boiler means it might never see higher than 50% fire except for a few hours per winter when it might see 70%.

So it's spending most of its time at the lower thermal efficiencies. That article from Raypak is assuming a perfect world where both the mod and the other boilers were sized for 100% at design load. This almost never happens in a residential setting.
As far as standby losses, it is a much larger issue in commercial where the heat lost off the boiler is truly lost to a well ventilated mechanical room. Most residential installations the boiler is in conditioned area so the heat is not really lost, it goes into the space that needs to be heated anyway.
Picture a single stage condensing boiler on outdoor reset with a buffer tank (or a high mass condensing boiler) that allowed a 15-20 minute cycle even in low load conditions. This boiler would always run at peak thermal efficiency, with water temps that were only high enough to meet the load on any given day. While I have never seen this setup I believe it would be the most efficient possible. John Siegenthaler has an article somewhere about it, maybe I can dig it up.