If I remember correctly, the Intel had lots of 8088s available immediately (so IBM could do things like lifecycle testing), and Motorola did not have enough 68000s available yet. IBM was concerned about how much memory you would be able to use with future iterations of the 99000.
The 68000 series did see use in the Macintosh, Amiga, Sharp X68000, and it completely dominated the Unix workstation space in the late 1980s. There were a lot of companies who thought, “I’ll buy a Unix license, buy some M68000s, and sell workstations.” Most of these companies disappeared. Later Unix workstations used all sorts of architectures.