16.10 has modified gcc to compile with -pie by default. That just must get in the way of unexec.
Search "gcc" in
https://wiki.ubuntu.com/YakketyYak/ReleaseNotes,
I have tried this successfully (both emacs-25 and master):
1. in the git workdir:
$ ./autogen.sh
2. in the build directory:
$ ...../configure CFLAGS=-no-pie <other configure options>
and the binaries built fine.
On topic, it would be nice if there was a string in the binary that told one how the $(config.status --config), so one could (more) easily rebuild a binary. Something like a function (emacs-configure-options).
This has worked with ASLR on (echo 2 > /proc/sys/kernel/randomize_va_space)
and with ASLR off (echo 0 > /proc/sys/kernel/randomize_va_space).
I hope this helps all to work with the new Ubuntu.