I thought the same thing originally, then I did my first compile. I think the reason is that there are many options when you compile. The first being Mame vs. MameUI, what type of OS, 32 bit vs 64 bit. There are also many optimization options for different processors and chipsets. Intel, AMD, Dual Core, Core 2 Duo, SSE+, SSE-, etc.
So there would be many compiles for each version and most of them are not compatible. Pick the wrong compile and it won't work on your system.