C:\Users\username\AppData\Roaming\MultiCommander\Config\MultiButtons.xml
No that is the User file, This files is loaded by MC if it exits.. If you edit buttons in MC, this file will be updated
The file under the install folder is the "Default" file that is used if the file under the account profile does not exists. So if the file C:\Users\username\AppData\Roaming\MultiCommander\Config\MultiButtons.xml does not exists. (As in a NEW fresh install) then it will copy the file from the install folder to the user profile and use that.
When you update MC. the file in the Install folder can be update. so the default layout can be changed. but as soon as you have a file under your user profile. that will not be copied over..
You should never modify the files under program files (install folder). They can always be overwritten by installer. They are default files to use if user copy of the file does not exists.
IF you run in portable mode. it is different. But then you do not have files under your user profile.