Autodist creates 'Makefile.am' files from 'Makefile.ad' files. A software project do not need to use 'Makefile.ad' files if there is no need to use distdef conditionals inside makefiles. Usually a multi distribution software project, however will need to define certain things to different distributions. In these cases 'Makefile.ad' file needs to be created.
Even though it would be possible to use distdef conditionals also inside 'Makefile.am' files, Autodist does not process 'Makefile.am' files when preparing the source tree for configuration and compilation (see Preparing source tree). Thus, the prepared environment would not be identical to the created distribution package (when the 'Makefile.am' will be processed), and configuration and compilation would be inconsistent. Basic rule is, if you need distdefs (see Distdefines) inside makefiles, put them inside 'Makefile.ad' file.