I imagine at the time, they were pissed. Constantly being bombarded with this bug that bug, and most of the people reporting bugs weren't even using MAME. They were using derivatives of MAME that modify stuff like MAME32, MAME Plus, and MAME blah blah. Sadly the first rule of reporting a bug, is to make sure you are using MAME and not a derivative.
At first this check was hard coded, then they listened to the users and and added the way to turn it off. If you've seen the MAME forums most of the bugs reported people aren't using official MAME or report things like bad graphics even when there is a big screen that comes up and says this game has incorrect graphics. They try to educate the user by displaying that message and allow them to disable it, it's not hard to disable it as you know, but it takes hopefully a little understanding and a little common sense which when you get people around computers seems to go out the door.
It gets tiring, I'm sure the devs around here feel the same. There is a reason they came up with RTFM.
Now, if you are talking about other things like artwork or what not, I dunno. What else do you change from the default?