Unfortunately it does not work because git apply does not commit the patch and tools/make_makefiles only takes committed files into account. So when make_makefiles is run it does not update configure.ac.
git apply suggests using git am to create a commit but git am compalins the patch is not in mbox format. There's probably a reasonably simple solution to that. Either that or modify make_makefiles to take into account uncommitted files but I don't know it that would be accepted by Alexandre.
It may also make sense to re-run make_makefiles and makedep when they are modified. It seems you've run into that one recently. This can totally go in a separate patch though.
Finally for anyone interested I updated the wtbsuite with 3 new patches around on this theme:
* WTBS kernel32:timer: Test + make_makefiles patch. https://github.com/fgouget/wine/commit/1b76e754b429256e9fd68c78e5134c4e2ff2e...
* WTBS kernel32:atom: Test + makedep patch. https://github.com/fgouget/wine/commit/67bfa38ec87496552f7bc9a4ebc9ff45b09f7...
* WTBS icmp:dummy: Add a new test directory. https://github.com/fgouget/wine/commit/4a4550554f11f8273dfc1cfcd0bc733d40898...
The wtbsuite is the test suite for the Wine TestBot. It consists of commits to a special Wine branch. You can pick any of the commit and submit a job to the TestBot to verify that it handles the patch correctly. One can get the test suite on GitHub:
https://github.com/fgouget/wine/commits/wtbsuite