Regardless of where the button mappings occur in the gae, at any tournament, there's going to be a number of people using all sorts of controllers, sticks, pads, hitboxes, etc.
Having a button mapped incorrectly doesn't count as a hardware malfunction in standard (Evo) tournament rules; if the button is mapped to an incorrect action, then that's on the player.
Given those two things, because you never know who was on the console before you and with what kind of custom controller/mappings, players go through button checks to make sure that all of the buttons on their controller map to the actions that they expect.
Granted, most sticks/pads nowadays map to the default mappings in most games (especially Capcom ones), and chances are that the player before you on the console had the "standard" mappings.
Of course, it's better to be safe than sorry.
Also, there are a number of people who turn off the KKK and PPP mappings, as hitting one of these means that you'll get a HK/HP (because of input priority) while some people want them turned on.
Pad players also tend to have very specific custom mappings, depending on their character and what buttons are more comfortable to them.