Gidday BM
Don't let the stealership snow you, mate!
I had to re-park SWMBO's SH Sportshift just a few minutes ago. Recalling your post, I took the opportunity to take it for a quick thrash around the block in full auto, sports and manual modes. Not the slightest signs of anything that could possibly be called a 'clunk'.
Smooth as silk in all modes, with none of the slight slip that our Camry auto box had.
Changed up and down with no hesitation, delay, slip, jolt, jump or other unusual noises or feeling/s.
IIWY, I would take it back to the dealer and require them to have it checked by an independent auto transmission expert. Or do that yourself first, and get a written report on it. You will almost certainly have to pay to have this done, but better to pay that small amount now rather than a highly expensive auto box rebuild after the warranty has expired ...
In fact, I would use the dealer's previous actions regarding your battery problem to demand that they pay for the independent report if things turn nasty ...
All the best with it, mate. These things are always a potential problem with s/h cars, which is why the statutory warranty provisions were introduced in most States around 25-30 years ago.