The hole in the tomato is pest/animal. The spots on the leaves are either fungal or bacterial (maybe septoria). Trim the affected leaves and spray with a fungicide to prevent further infection.

Could be a fungal infection. Succulents are fairly good at sealing off fungal infections if they are minor--you end up with a dried up black spot like that. Watch the humidity in the air--cut back water when it is hot and humid. Make sure succulent plants get plenty of light, and watch for scale insects and mealy bugs which can damage or kill plants.

Not an issue. Just plant it like you would any transplant. If you really want to do something, dust it with rooting hormone.

Obviously you can reject my answer if you wish but I stand by it. I've been growing and reading about growing for many decades too and I have seen this phenomenon. What you see in your images is the callus formation which is part of the indirect organogenesis process. As to the mush there's nothing to say there can't be some rot as well as the incipient roots. Perhaps if it ever happens again you could keep the cuttings and see what happens.