From the document you've already found, the MC68F396 is similar to the MC68376, except it has SCIM2, TPU2, CTM4, 8k SRAM, 132k of FLASH and FLASH for the TPU as well. That's unusual to have Flash in a 68k part like that way back then (1998 or before).
It is actually a pretty good match for a high-end MC68HC16Y3 or MC68HC916Y3 (they have SCIM2, TPU2, Flash SRAM) with the CPU16 replaced by a CPU32. I suspect it was an MC68HC916Y3 with the core replaced, made for a specific customer with a requirement for that CPU. You could try and read the MC68376 and MC68HC16Y3 manuals for hints.
I'm surprised at how little information exists for this part. What does the OP want this information for? I don't see how you could reprogram one of these, even if you could get it or the data sheets.
Here's a mention in EDN in 1998: "MC68376 and the flash MC68F396"
https://www.edn.com/08-17-98-can-protocol-eases-automotive-electronics-networking/
Here's someone who was working on a project using one in 1998:
https://es.linkedin.com/in/mark-lindsay-85ab4018
Nothing in comp.sys.m68k.
A 2000 version of some GCC documentation mentions support for it (based on the CPU core only):
[E Book] Linux, G C C X G C C The Gnu C C++ Language System …
Someone posting in 2008 that some engine controllers used this chip - maybe they were the specific customer:
https://www.usbjtag.com/vbforum/showthread.php?t=1871
Motorola spun off Freescale in 2004. Maybe that product didn't make it across? I can't find anything on archive.org, as Motorola's SPS division's web pages were never searchable using archive.org.
Lauterbach supports everything else, but not that one:
https://www2.lauterbach.com/pdf/ice_68330.pdf
Tom