I would bet it would have worked the exact same way. Compaq's success was the BIOS and Microsoft's willingness to license DOS, and those wouldn't have been changed with the 68008. Given IBM's want for the 48 pin package, Compaq might have had a more interesting machine with the full 68000.
It doesn't matter if it was about the BIOS or whatever else, had IBM won there would be no clone market.
Microsoft could have tried to make MS-DOS portable similar to CP/M or UNIX, but it would be a big what-if regarding Amiga, Atari, Mac, Archimedes and UNIX market.
Had IBM won, most of the fair use we take for granted would have gone out the window. The modern day version of that lawsuit was Oracle vs Google. Compaq started the clone market and I see no reason that their strategy would have been altered in a Motorola vs Intel world.
On my alternative universe, the same people that decided to pick Motorola might also have had the perspicacity of putting in place the mechanism to prevent such actions.
