1. Based on Kellogg's verbiage, anytime you have ASME Flanges, where diameter of effective gasket reaction is defined.
In practice, I find Kellogg's Peq method to be all but unhelpful as it tends to add forces and moments on top of design pressure. 95% of the time, the process conditions handed to stress are the same as the pipe spec pressure, and 95% of the time, the pipe spec pressure uses the flange as the limiting factor, and they're now asking to get allowable loads when it's already maxed out or nearly maxed out.
2. There are any number of reasons we could speculate upon, and there could be as many reasons as there are user specifications. Ultimately, the most logical will be there is no caretaker of the specification that has the capacity to perform research projects necessary to validate it. Some simply aren't willing to put themselves at professional risk by "bucking trends."
3. As an analyst acting as an agent for ensuring piping code compliance, and piping code typically include verbiage for guaranteeing components of the piping system, such as flanges, if the compressive force could result in failure, then you would be seen as responsible for not foreseeing the flange's leakage or failure.
Generally, you won't see leakage due to compressive load while a compressive load is applied (assuming everything else is copacetic), but it is feasible to theoretically bend a flange face with a sufficient enough compressive force combined with what would otherwise be a moderate moment, in "simplified" analysis, and then you could see flange leakage, going back to "normal" operation after a given upset condition. But the pipe would have to have a certain level of beefiness compared to the flange to accomplish this.
The larger the diameter and the lower the pressure, the more likely this could be a problem.
I'd also point out that gasket misalignment and high compressive loads could have serious impact, but we're in for an infinite recursion cycle if we had to analyze for every potential installation mistake outside our control.