I’m not sure about everything else, but the “.config” is the main configuration and it is comletely missing. It looks like you are on a 64-bit x86 host cross compiling for 32-bit Jetson TK1. If you look at a working TK1, there will be a file “/proc/config.gz”. This is a compressed version of a working configuration…you can copy this to your kernel source and gunzip it, then rename to “.config”. Any changes needed in kernel config can then be started with that config and whatever edits you want (e.g., “make menuconfig”).
At the moment I’m in the process of upgrading my host from Fedora 19 to Fedora 23, and do not have my cross compile tools in yet, so I can’t actually test. What I’d look at is if DESTDIR is writable by you. Then I wonder if perhaps the .config is just in the wrong place. Have you tried manually placing the .config rather than using tegra12_defconfig?
Bumping this, I’m not set up to answer cross compile questions until I get my workstation upgrade finished and the thread was previously in the legacy forum.