I did a full rebuild with the 4.8.1 kernel bump which grabbed the correct/updated files and I now see the file timestamps matching other items which are normally updated as part of an OS update:
Slice2:~ # ls -l /flash/total 133800
-rwxr-xr-x 1 root root 1494 Oct 15 11:35 LICENCE.broadcom
-rwxr-xr-x 1 root root 126730240 Jan 1 1980 SYSTEM
-rwxr-xr-x 1 root root 48 Oct 1 13:07 SYSTEM.md5
-rwxr-xr-x 1 root root 13743 Oct 15 11:35 bcm2709-rpi-2-b.dtb
-rwxr-xr-x 1 root root 14417 Oct 15 11:35 bcm2710-rpi-3-b.dtb
-rwxr-xr-x 1 root root 13717 Oct 15 11:35 bcm2710-rpi-cm3.dtb
-rwxr-xr-x 1 root root 17932 Oct 15 11:35 bootcode.bin
-rwxr-xr-x 1 root root 47 Oct 1 13:07 cmdline.txt
-rwxr-xr-x 1 root root 3365 Oct 14 22:57 config.txt
-rwxr-xr-x 1 root root 1027 Oct 15 11:35 distroconfig.txt
-rwxr-xr-x 1 root root 4451 Oct 15 11:35 dt-blob.bin
-rwxr-xr-x 1 root root 9737 Oct 15 11:35 fixup.dat
-rwxr-xr-x 1 root root 6222256 Jan 1 1980 kernel.img
-rwxr-xr-x 1 root root 48 Oct 1 13:07 kernel.img.md5
drwxr-xr-x 2 root root 8192 Oct 15 11:35 overlays
-rwxr-xr-x 1 root root 3895684 Oct 15 11:35 start.elf
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image files on the webserver are still named 7.90.007 but are updated.. would be great if you can do the full update test.