Often countries charge visa fee equal to what the other country charges their nationals. Hence the wide range of fees for identical services in some cases.

As for the flight comfort, you have to check on an individual flight basis. There is some diversity. Most are operated with 2 class regional J, but some are with 3 class aircraft (scheduled) and others often have substitutions. So there is a pattern -- but I don't know what it is, as I don't fly these routes. For example some HKG-BKK flights are much better than others and at least one is operated by an A340 sold as 3-class. It does vary by day of the week even for the same flight number (EQV really does mean equipment varies on CX).