@SlowSL MAME GUI seems to generate additve "OR" keymaps while you remain on that line for input. If I want to remap a control, I simply move up or down to the next one, then back to the one I want to edit and remap. This always replaces what is there starting with a fresh mapping. If you just keep pressing ENTER on the same line they combine (as you noticed).
Sometimes, I will combine stuff intentionally. For example, I might combine coin drops when playing from the vertical ends of my cabinet (3-sided cocktail design). I might also map multiple action buttons for a game to give the player the option to hit one button or another button for the same function.
Understanding the "null" mapping in per-rom .cfg files is also really useful, as it blocks the retropad mapping and allows just the raw key inputs to reach the MAME GUI. This is necessary if you want to do complex boolean mapping (with "NOT" settings for example to setup a tankstick).