Note 1: Genode seems to get latest version of Nova by a simple git
clone without mentioning the revision that it seems to be done for:
genode-master/base-nova/Makefile:
GIT_URL = git://github.com/IntelLabs/NOVA.git
GIT_REV = 16dd65c15dac298dc5b36d636d79fa0110bd5736
...
$(CONTRIB_DIR)/.git:
$(VERBOSE)git clone $(GIT_URL) $(CONTRIB_DIR)
which seems to ignore GIT_REV

You are missing the next block in that file: In this line (https://github.com/genodelabs/genode/blob/master/base-nova/Makefile#L43) and two lines after the clone is reset to the revision specified in GIT_REV and then the custom patches are applied.