I am now concerned the keel hull joint was compromised. Any thoughts appreciated.
I think you can rest assured that there's about a zero % chance the yard damaged your keel. You can't lift the boat by the keel in the manner you describe. The leading/trailing edges of the keel are too steep--the straps of the lift can't grab them, so they just slide up the keel's fore/aft edges until they meet something horizontal. The horizontal surface they meet is the part of the hull called the keel boss (or keel stub).

It's the strongest part of the boat--a combination of thickened fiberglass, the box-beam structures of the TAFG, and the thick fiberglass shell of the hull itself. It was designed to support the 5200lb keel, not only vertically, but also when the mast is tipping the keel to one side while a wall of water is pushing it to the other (all, likely, while the boat is also pitching up and down along the waves).
So, even if you could lift the boat by the keel alone, it would harm neither the keel nor the hull.
As for cracks, here's what my keel joint looked like at the last haul-out:

The yard picked out the "loose" sections of barrier coat/filler/previous patching materials, then re-filled the voids with Sikaflex and re-painted. At the previous haul-out, I did nothing more than paint over the cracks.
My theory on the cracks? The barrier-coating Ericson applied over the fiberglass (and, I believe the keel) seems extremely brittle. Slight movements cause it to crack.
This is what my prop strut looked like when I bought the boat in 2016.

The surveyor tried to shake the strut by hand, saw no movement, and declared it "good." I've never had problems with that area--I just re-coat it with bottom paint at each haul-out.