Retroarch arcade control mapping is a long story : configuration, overrides per game and core, retroarch.cfg in different folders, remaps and core options.

For the mame2003plus core is a nice feaature which gives best arcade mapping for the layout

Y X L B A R

goto to Setting, Input, Input User x Binds and select as User x Device Type the 6 Button option. It shows up in retroarch.cfg as

input_libretro_device_p1 = 769

everything works as expected from my point of view.

y = button 1 x = button 2 L = button 3 B = button 4 A = button 5 R = button 6

Other emulators have Fire 1 or jump on retropad B or A, means on button 4 or button5. Have in mind that we are talking about a arcade machine, perhaps with Jamma interface. Means that we have only 3 button. So all game can not be played since Fire 1 is on button 4 which does not exists at all on this machines. Or image a neogeo cab. Hey neogeo coooool: 4 Button Control Panel. So how to play games that needs more than 1 button? Fire 2 is mapped to button 5 ;)

For this emulators like mame2000, mame2003 or lr-fbalpha I have made some thousands of remaps.

Who does not know this retroarch message :) I get rid of it when turning the automatic overrides on and off again. Weired, but works.