I think the reason for the worse mileage with the 3FE is mostly due to the engine being a very old design that is fairly inefficient with fuel, but extremely over designed and over built for durability, which was it’s primary design parameters.
The 1FZ was specificly designed to be a direct replacement of the 3FE, meeting all the same design parameters, including longevity, simplicity, low end torque bias, but primarily making more power, with weight reduction if possible. It even had to be nearly the exact same size as the 3FE, in terms of overall dimensions. Improving fuel economy was a plus, but back in the late 1980s, when fuel was still cheap, it was not a major priority.
The primary vehicle for the 1FZ was the same as the 3F/3FE, the 70 series Land Cruiser and the 80 series. Most of these vehicles were sold as commercial vehicles, used in harsh conditions in 3rd world countries.
So, the requirements for both of those engines are far different than an engine designed for and destined for the U.S. market, much less one that was designed today.
Here's my 1FZ page, with a few more details.
ExpeditionLandCruiserFZJ80engine
I'm sure if you put the 1FZ or 3FE into a lighter vehicle, mileage will improve somewhat, but both are fairly large displacement engines, especially the 1FZ at 4.5 liters, so its going to drink gas no matter what. There are large displacment engines today that can get much better gas mileage by using technology that reduces the displacement of the engine and the required fuel at highway speeds when the power is not needed, effectively making the engine run like it was a smaller engine.
What you get instead of fuel economy with the 3FE and 1FZ are engines that will run in any part of the world, under nearly any conditions, drink nearly any 3rd world fuel, and run for nearly half a million miles and several decades or longer of very hard use. That's specificly what they were designed for. the 3FE and 1FZ were not designed specificly for the U.S. market like engines we see today are.
When Toyota came out with the 2UZ, it was primarily designed for the North American market for use in the new North American exclusive full size Toyota truck and SUVs. The design parameters were far different. Now, fuel economy and over all power was the primary concern, along with general Toyota reliability and longevity. the 2UZ found itself in the Land Cruiser 100, because it too evolved into less of a commercial vehicle and more of a luxery SUV in all markets. But the 1FZ was retained for use in the 70 series and even the 100 series versions that were primarily sold as commercial vehicles and is still in production today for certain models.