That's how I run my flail. Run an extended top link, mounted in the fixed hole, under compression to keep the unit rotated back onto the rear roller, and let the 3pt float all the way down. It works best for me. It allows the unit to float with changing terrain throughout the entire height range allowed by the 3pt without touching the lever. Took me a couple of trial and error adjustments, but now I know exactly what angle to set via the top link to get a nice close cut without any scalping or gouging.
Sure, the top link is normally under compression, but only as much as it is holding the unit back from forward rotation. Any more force that gets transmitted into the top link turns into lift of the 3pt, so that compressive force is sort of self limiting... and surely isn't any greater than what it would see running a middle buster or plow. There is a condition that would compress it a lot more. Backing into a hill so steep that you run out of 3pt height! Since the flail isn't all that long behind the tractor, that would have to be a pretty dang steep approach angle to ride the flail up higher than my 3pt range allows. So I don't see me pretzeling my top link any time soon. I guess another condition that would do it is hanging on a stump or something with the unit, but that's going to tear stuff up regardless.
I tried it the other way; setting a reasonable height with the 3pt and letting the top link float in the slot. I did not like this configuration for a couple of reasons. #1 - It does not follow rolling terrain as well beyond a very small range (the angle of rotation allowed by the top link floating slot, which isn't much). #2 - To deal with #1 you must manually adjust the 3pt height for various terrain changes, and it's not easy to pinpoint the height back to what you wanted it at when things level out again.
For your additional consideration, my flail unit has little vertically floating links where it attaches to the lower 3pt arms. Well, they come pinned so they don't float, but I unpinned them. This allows the unit to raise or lower a couple of inches on either side independently. The result is that the unit can also follow the terrain some in a twisting motion. I can drive diagonally across a drainage swale or bar ditch and the unit mows pretty evenly all the way across without me having to touch anything. Setting height by raising the 3pt and letting the top link float would eliminate this benefit, as those little vertically floating links would be held up against their stops all the time.
Anyway, like I said above it's what I've decided works best for me after trying and analyzing the pros and cons of both configurations.
xtn