Good question. It's like when folks put clear plastic covers on their sofas. They want to keep them nice.
But in this case. It's an ugly nagahide cover over the sofa. Otherwise I'm enjoying the car. It replaced a FJ Cruiser that was lucky if it saw 16mpg.
On the Gen 2, you can take the trim rings off (which I did). Looks much better. Any reason why you can't do the same with your "plastics"?
Aerodynamics seems to be why they are there, you can decide ugly is worse than whatever MPG hit there may be.
Darell (evnut on this forum) found data indicating less than ½ a mile per gallon loss, on the gen II, while driving @ freeway speeds. Probably similar for gen III. Roughly 1%. Statistics say it's nothing - if it's under 5%, so I say chuck 'em ... that's what we did. And welcome! .
If the difference in drag is really that small at steady high speeds, then they may well have slightly detrimental net effect on fuel consumption during low-speed stop-and-go urban conditions or on hills, because of their weight. But if the difference in drag is really that small, why does Toyota spend their money on them, when their aesthetics are so unpopular?