Here is the screenshot of the new implementation, which is way better done, and allow to add a comment in a tooltip. For now, the tooltip only shows when the text is hovered, because otherwise it prevents to read the text behind the tooltip. I used wavy line for "underline-only" and straight line for commented ones, but this could now be changed very easily.
Also, the new implement should prevent much errors, as it doesn't modify the original message. But this feature is complex and took way more time to implement than expected.
Small visual tweaks (but I can try to do it myself if needed):
underline button: probably not possible, but it would be even clearer with a red line under the U
tooltip: I'd use a normal white background - black font
wavy red underline -> great
for "comments" underline: wavy blue (or another colour, yellow..., as long as it's not red) => to make it clear that it's a comment, similar to the wavy red markup, but that it's not necessarily an error (the comment will say).