They're currently being applied like this:
$this->bbcode_second_pass_code('', 'git apply ../0001-my.patch')
The kernel tarballs however aren't actually working git repos. git still attempts to apply the patch, but it's very brittle.
Building outside the PKGBUILD git tree seems to work fine. Unfortunately when in-tree, git seems to get confused and doesn't apply the patch correctly. Patching fails without any indication whatsoever.
Lost quite some time figuring out why a kernel that worked fine when built by hand, failed to boot when built via PKGBUILD.... Turns out my patch wasn't being applied

The solution IMHO seems to be just using patch directly, just like it's done in Archlinux:
$this->bbcode_second_pass_code('', 'patch -Np1 < ../0001-my.patch')