You're right, the 68000 shipped before the 68008. Still, the 6809 instruction set only resembles the 68000 set in a superficial way, the registers are completely different and even though they are technically of the same family they'd have to start all over again. Somewhere along the line they must have decided they needed more memory (and accessible faster than bankswitching could provide) so they ditched the 6809 in favor of the 68000 family.
So, it went 6809->68000->PowerPc->x86.
It's stranger still because the development of the Lisa started around that time as well and that did have a 68000.