I'm dealing with the same thing. My shop said I needed to replace the piston. It's annoying, but it doesn't seem to affect drivability, as it has been like this for some time.
I did the pan drop with the filter change and refilled. I too thought I needed to treat it like an oil change and get nearly all the fluid out.
However, my research shows that the new ATF fluid you add will have enough detergents and friction modifiers to rejuvenate the overall quality of all...
I wonder if where you regularly fill up the vehicle has clean and well-maintained diesel storage tanks? You hear about people occasionally in the US getting a bad tank of diesel with too much water content so they have to go change their fuel filter and such. Diesel is more susceptible to this...
Another vote for Toyo Open Country A/T III's. I have done a lot of off-roading and road trips in my GX and previous Tacoma with these tires and have been quite impressed.
There are no lights or leaks, either. Everything is working fine, just rather annoying. My shop said it looked like I somehow damaged the shock itself internally. I need to find one from a crashed car, as brand new ones are quite expensive.
I haven't found the AC to be overly impressive on my 2018, I had it recharged a year ago, and it was a bit low on freon. Once again, it does an okay job but not like some cars that will freeze you out.
My front KDSS shock is super clunky; I think I may have damaged the internal piston/rod off-roading. Changing direction or pretty much any form of movement makes itself known. It doesn't seem to cause any driving issues other than it's quite annoying; I need to change it, though.