You are focusing only on the cubic inch numbers and there's more to it than that. The FE engine family came to be in the late 50s and spans the 352, 360, 390, 406, 410, 427 and 428 cid derivatives. These are muscle-prone cast iron heavyweights that proved themselves in NASCAR well into the 70s and are, for Cobra purists, the Holy Grail. The 351 is part of the small block Ford family, evolving from the smaller 289/302 family and taking root during and after the early 70s gas crunch as the staple V-8 for Ford. Through stroking and boring the 351-based engine has yielded a number of large cubic inch engines, including the 427 "Windsor." You can also bore a 427FE up to larger cubes and they can be stroked as well, producing stupendous amounts of torque. The 427 FE and the 427 Windsor have the same cubic inch displacement, but they are as different as a chicken and a rhino (you can pick which is which.)
As mentioned earlier each have unique power and torque characteristics, and each have their pros and cons. The FE is a bit larger and heavier, generates more heat, is harder to find in original condition, etc. The Windsor is smaller, lighter, parts are plentiful and fairly priced. Some guys choose FEs to be period-correct, some just like fixing leaks all the time.
Some simply can't afford FEs or don't want to learn how to babysit their unique characteristics. Some could care less about period-correctness and just want the most power for the least $.
You should decide whether or not a period-correct engine platform is part of your finished car objectives. If not, the 351/427W might be for you. If you want to have the same 427 in your car that was available in the 60s, then you want the FE. As you are about to see in this thread, the Kirkham and FE are considered by many to be synonymous.