I get virtually no warnings (in the AFNI code proper) with my builds with gcc on Linux and Mac and Solaris. Without more information, it is impossible to decide if the warnings you are seeing are problematic.
In general, I do not like "patches" that are to be applied with the patch program. They just leave me feeling "ucky". This reaction is irrational, and cannot be overcome by reasoned argumentation.
If you wish to make changes to an AFNI file, you should
(a) make sure you have the latest version from this AFNI site
(b) let us know you are about to make the change
(c) make the change and send us the changed file
in toto
This issue hasn't arisen much in the past, though, since most people are content to be consumers.