The patch in summary is touching both Makefile.in and Makefile.am, probably to avoid autotools rebuild.
This treatment is usually reserved for a few selected system packages that cannot have their autotool scripts rebuilt.
This _could_ cause maintainermode-driven rebuild (see http://blog.flameeyes.eu/articles/2008/06/13/maintaner-mode ), which is something we should be avoiding as much as possible.
Please just patch Makefile.am and/or configure.in/.ac and rebuild autotools, unless you have very good reasons not to.
I'm sorry, but there is no technical reason this could cause any problems, other than getting the emerge succeed too fast thanks to the lack of an eautoreconf call.
Feel free to open with a technical reason for not patching Makefile.in's, and
therefore forcing to use eautoreconf and a longer emerge time on users.