section infiletypes.cpp, then custom entries for the Set Build Commands dialogue can be configured to be the same for all new projects. However, this does not happen.
Settings in the user filetypes files are not copied to projects, they will be used if there are no settings in project to override them, they show in the project properties build tab as greyed and can be overwritten to create a setting in the project that hides the filetypes setting. So if your new project file has no settings in the build section it should use the filetypes file settings.
The filetypes dependent commands are of course only used if the file is the right type. For filetype independent commands the settings are taken from the user `geany.conf` if there is no setting in the project file.