That is about how both the 540 and 800 are adjusted as far as length. They both weigh exactly 3.0 lbs.
The 800 has a straight shaft and the 540 has the 90 degree offset. Maybe my right arm is just used to the 800 straight shaft since I have been using it since March 2018 and the 540 only a few times.
Those are the only two things that can account for the difference as far as I can tell.
Not sure what the solution is to my problem though. Certainly don't want to use a swing harness for the 540 just on the stock coil.
Waltr is mostly likely right - balance is probably the issue. Length and overall weight, while certainly important, aren't the only parameters that define balance, and by direct extension, long term comfort for swinging a detector. The position of the fulcrum relative to the center of gravity of the machine plays a massive role in the feel of a detector, as well. A simple and exaggerated example would be a broom stick. Try holding a broom by the very end of the handle and hold it straight out parallel with the ground with the bristles pointed away from you. Then hold the same broom parallel to the ground with your hand positioned on the handle closer to the bristles. Which one would you rather hold all day? Same broom - same length and same weight, but vastly different balance and fatigue level to carry it.
Same thing applies to your metal detectors - with the difference in the shaft shape, the Vanquish and the Equinox surely have a different center of gravity right out of the box. I don't know how the 540's stock coil weight compares to an Equinox stock coil, but any difference in weight gets greatly magnified since it's hanging way out on the end of the shaft (remember the old physics formula, weight x arm = moment...or add a little more weight to the end of the broom in the example above). This is why a larger, heavier coil always makes any detector feel at least a little more nose heavy with all other things being equal. If the Vanquish coil weighs more than the Equinox coil...more nose heaviness and more fatigue.
Weight distribution behind the fulcrum (essentially the handgrip) is important for the same reasons...for example, the distance of the cuff from the handgrip, along with the percentage of the total detector weight massed there, and how all that is oriented to the center of gravity is a factor. I'll guess the shape of the 540's shaft automatically makes for a different feel between the two detectors even if the cuff distance is the same.
Moral of the story - don't underestimate how much even minor differences in weight distribution can impact the feel and comfort of a detector, even two different detectors of the same weight. With proper balance, even a heavier machine can feel more comfortable in the long haul.
I own an Equinox 800 with an aftermarket straight shaft. I've always been comfortable swinging the machine with both the 6" and 11" coils on long hunts, but when I recently bought the 15" coil I decided to be proactive and purchase a counterweight from the shaft manufacturer. It improved the feel of the 15" coil so much, I tried the counterweight with the 11" coil too. I was amazed...swinging was virtually effortless! I had no idea how much work I was actually doing with the stock 11", even though it was comfortable. Yep, I made the machine a few ounces heavier...but I greatly improved the balance.
If it's truly bothersome for you, it would be easy to experiment with some weight on the shaft to help. Just strapping some weight under the arm cuff can be enough to give you an idea, and it probably won't take much. Depending on the parameters Monte mentioned (shaft length, your height, etc) you'll probably find you only need a few ounces to make the 540 feel similar to what you've been used to with the 800. Or add more, and improve balance even more.
But maybe start simple. Monte's info is very important also, and it might be worth taking a closer look at your swing and how far the coil is from your feet when you're swinging each machine. Because the shafts are shaped differently, you might find that you're actually swinging the 540 with a different overall geometry that's actually causing fatigue even thought the shafts are extended the same length.