If you need to do cloning-type operations that are greater than LR/ACR, eg content aware fill, then PS gives you many ways to work.
My preference is not to use merge visible as it's the whole layer. Instead I'll use the marquee/lasso etc to roughly select the area where I need to clone, maybe feather the edges with Selection > Modify > Feather, use Ctrl or Cmd J to copy the selection into its own layer, and then I'll do the cloning on this smaller layer. I'll do this for each area that I want to do something on, and in the latest version of PS you'll see the new Edit > Content Aware Fill command does the same thing, putting its output into its own layer. So it's easy to redo or scrap each individual bit of work.
If you re-edit the SO, there is a big problem if you've done cloning on a full layer created by Merge Visible. With these individual layers, you often have less of a problem. Some might need redoing, others not. But you minimise this by getting the original SO right first time, and experience helps here.
I'm not sure about your follow-up. I'd just send the file from LR as a tif, save it, then later in LR I'd do Edit > Send to PS and choose Original.
