Thanks David. After I submitted the ticket, Yoast seemed to release 2 hotfixes in quick succession that fixed some of the issue (word count on the page I showed went from 473 to 303). I scanned their Github and found that it seems one of their own devs discovered the issue and has it pegged for resolution in the next major patch (3.1) and not something of immediate concern. This isn’t just affecting your framework either, but anything that uses shortcodes.
Seems to me like something they would want to fix immediately, but the issue was found 2 weeks ago and they have no target date for the release of 3.1.
Thanks for your help as always.