patching Makefile.am: autoreconf or more patches?

[Edgar Fuß <ef%math.uni-bonn.de@localhost>]

While working on collectd (pkgsrc-ing more plugins) I noticed that 
Makefile.common contains a pre-configure target running autoreconf, 
presumably because there's a patch to Makefile.ac.

Since running autoreconf is rather expensive, wouldn't it be prefrerrable 
to include patches for the generated files (whatever they are) instead?
Or is this deemed to error-prone in case the patch to Makefile.ac is 
altered?