A typical bootstrap might also run libtoolize or autoheader . It is also important for all developers on a project to have the same versions of the tools installed so that these rules don't inadvertantly cause problems due to differences between tool versions. This version skew problem turns out to be fairly significant in the field. So, automake provides a way to disable these rules by default, while still allowing users to enable them when they know their environment is set up correctly. Note that maintainer mode is a controversial feature.
Some people like to use it because it causes fewer bug reports in some situations.
For instance, CVS does not preserve relative timestamps on files. When maintainer mode is not in use, the Automake-supplied missing script will be used to warn users when it appears that they need a maintainer tool that they do not have. The approach you take depends strongly on the social structures surrounding your project.