The version within the Makefile is this:
KERNELVERSION = $(VERSION)$(if $(PATCHLEVEL),.$(PATCHLEVEL)$(if $(SUBLEVEL),.$(SUBLEVEL)))$(EXTRAVERSION)
Normally “EXTRAVERSION” is empty, but something you are working on might set this in a Makefile. Default is empty:
A typical result from this is “3.10.96”.
After that CONFIG_LOCALVERSION is appended. Somewhere between Makefile EXTRAVERSION and CONFIG_LOCALVERSION is where anything beyond “3.10.96” is set. You probably want to check any Makefile and be sure EXTRAVERSION is not set.
I think JetPack can deal with kernel source, but the flash step itself just uses a previously compiled kernel. Headers would make no difference except when compiling modules from outside of the kernel source tree. That URL’s step 9 is designed to make sure any version info in a Makefile or Kconfig file match for cases of using separate headers.
Basically something part of the kernel source uses the normal kernel compile with its own headers, Makefile, and Kconfig; separate headers would be used for third party driver compiles or for compiles of anything tied to kernel headers when full kernel source is either not available or not required (and this implies separate Makefile and Kconfig as well). Should headers and source code differ things may not work well…versioning can be a way to determine if there are modifications. I have not used that “step 9” from the URL, but it seems the step is designed to keep headers matching source when separate headers are used instead of full kernel source. Between EXTRAVERSION and CONFIG_LOCALVERSION the final source and headers must match…the repackaging of headers accomplishes this and is unnecessary when using full source. You’ll have to figure out if a Makefile EXTRAVERSION exists in the headers, and if it does, make sure it matches your installed system. Same for CONFIG_LOCALVERSION (CONFIG_LOCALVERSION is part of Kconfig, EXTRAVERSION is part of the Makefile).