This may be a month late, but I have a 2015 sa424, and I have always had a bit of a clank when engaging; I don't like it either, but I'm oddly comforted that you have the same issue, as I had often thought mine was abused at the new-tractor lot before it was purchased. I think there is a bit of play built in as part of the hydraulic coupling to the rear PTO output shaft, but I have not seen an exploded diagram to verify. It will be good to see what your 50 hour checkup indicates.
One of the best investments I made was a slip clutch on the rear PTO. Because of that aforementioned play, if I engaged or disengaged too quickly, the bounce was likely as not to add momentum that sheared off my pins more frequently than I thought was normal. Going to a grade5 shear bolt seemed like it defeated the purpose, I would much rather keep replacing pins than replace drivetrain components. But it always made me cringe.
Enter the slip clutch.
The downside is that you have to carefully make very sure that your PTO shaft doesn't bottom out on each implement, because it makes the PTO output much nearer to the implement, so a too-long shaft is going to damage something when you go through the minimum (at parallel). So when you install each implement, raise it up to parallel, and compare the length of the shaft next to the installed clutch. If it's too long at its shortest, you'll need to take a little bit of length off th shaft until it has sufficient clearance. (If you are using an add-on quick-hitch adapter, this may not be an issue, but you should repeat the procedure to make sure you have good shaft length with and without the 3-pt quick-hitch).
Also it makes it hard to glance at the fluid level window from a distance.
Now the upside. The transition is much smoother on my 4x10
chipper and my 4' brush hog, both of which ave a lot of momentum in either direction. With the clutch, it may slip just a bit on startup, then catches up immediately. If I stuff the
chipper with a branch that is too much, it may stall the tractor, but it's a gradual stall, so I have a chance as it's bogging down to pull the branch out, and I know that the sliding force is much easier on things than zero-yield components.