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patching autoreconf or more patches?

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

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 is 

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