The secondary-selection is used when the cursor is in some focussed Recipient window, in order to grab some text (or whatever) from some Donor window (possibly the same window as the Recipient) and have that text pasted at the Recipient’s insertion-point (overwriting any primary-selection in the Recipient).
I assumed primary is ctrl-c/ctrl-v and secondary is select/middle-click. I’ve never come across this ctrl-middle-click, it does the same with and without the ctrl key.
I seen to recall reading something this week about a distro dropping middle click, so I probably conflated both issues and failed.
But you’re right, I did not read the fine article.