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Article sounds like the author's opinion and never states HOW he determined these things. I have never been on a flight where someone gets upgraded AFTER being seated. #3 seems like they are confusing the check-in process with boarding. I almost never interact with other passengers prior to boarding and certainly not when doing check-in. Clearly if the plane is full, there won't be many/any seats to do upgrades (#5) which seems rather obvious. Upgrading your seat with miles is how it works for EVERYONE..............IF you have enough miles, you can upgrade your seat. Anyone who flies and has accumulated miles already knows that.
I think the article would be more credible if he listed his sources. For example, did he ever interview any airline employees to get their input about how upgrades are actually handled?