It is possible she used more than one FPGA - like one FPGA for one custom chip replacement. Plus, the whole custom chipset probably isn't much larger than 8kLE, of course if you don't include the 68k CPU.
Minimig has a lot of special features added that weren't present it the original custom chips. Plus, since the minimig design is based on guesses at what the custom chips actually do inside, it is possible it uses (a lot?) more gates than the original design. Obviously, if you take into consideration when the Amiga custom chips were made, and that they were hand-drawn, 8kLEs (which could be as much as two to three times as much ASIC gates - so ~20k gates) starts to sound quite a lot
So the custom chips design prints could still be useful to see what some of them are actually doing inside, like what kind of pipelining, if any, is used inside, etc.
Do have to admit, I like Jeri and her work