Currently it's mandated that patches and scripts live in the root directory of the source, i.e. /usr/src/mod-ver/. No other locations are supported. However this is somewhat of a problem if /usr/src/mod-ver/ is managed by a package manager. Package managers usually make no guarantees that files placed here won't be deleted or overwritten, so manually changing stuff here is generally frowned upon.
Considering that there's already support for dkms.conf override in /etc/dkms/, I think it'd be a good idea to extend this a bit so that custom patches and scripts can be placed here too.