I do not remember the exact number of transistors in MC 68000, but I think that it was less than 40000, so not just slightly smaller. In any case, it had more than twice as many transistors as Zilog Z8000, which was super-optimized for size (a very bad decision of Zilog, which lead to a too long time-to-market and to many initial bugs), and slightly more than 4/3 times as many transistors as Intel 8086.

The 68000 transistors number claimed by the Motorola marketing was close to what you get by dividing the die area to the area of one transistor, so it did not correspond to actual transistor positions.

The MC68000 die had large areas occupied with microprogram ROMs, and there as you say only a part of the array of transistors are active, depending on the stored bits. Nonetheless, a significant part of the die was occupied with random logic, where all the physical transistors are used and a part of the area does not have any transistors.