The problem with this is that the original post doesn't say "I have a site that was crashing and locking up all the time, so I took it to WPEngine." It says "I have a site that was running fine on a VPS at Linode, but I got tired of the hassle of managing the VPS, so I took it to WPEngine."
The original post is written by the complainant, of course, so it's possible it's subjective or slanted. But if it's correct on this point, I don't think it's unreasonable for a competent party -- in this case, a person with a WordPress site that runs acceptably on a commodity VPS -- to expect that it would run acceptably on WPEngine as well. Presumably performance killers like the ones you cite would be just as bad on the VPS -- if not worse, since it's unlikely that a VPS' operator will be able to tune MySQL, PHP, Apache, etc. to the degree that an expert at a place like WPEngine would.