I see that you posted this update in November last year. It's now late April 2023 and this bug has not been fixed. This is of course frustrating, but sadly it's also not surprising given the long list of partially developed features we've seen going live over the years. The assignment comment library is another excellent example of a feature that people wanted but that on release was only half built and has languished since then receiving no updates at all.
Instructure, we really need you to address feedback on these features in a timely manner, especially when they very clearly interfere with functionality. I also want to push back on the idea that this is a bug rather than a really bad design choice. It would be a bug if the emoji selector was supposed to be showing up in another part of the UI. I don't see any evidence that this is the case. The slightly transparency on the selector which goes away on mouse over definitely looks like the designers, for reasons that are beyond my ability to guess, decided to place this button here instead of in the row of buttons below the box where it very clearly belongs so that it won't cover up text as you are composing comments. This definitely needs to be fixed, the fix is not a complex one, but for some reason it has remained unfixed for most of a year.