Either give an option to increase fade time on the message log, or make it so that repeat message logs (Specifically the ones that tell you "There is nothing to quick interact/attack here") don't flood when you use a particular input alot (Which you might when you're looting an area quickly)
Not sure if Godot can flag messages then check if that flagged message has finished being presented in the log, or if there's any possiblity of lockout timers on specific messages (Just the ones for the quick loot/quick attack, tbh), but if there is that'd be the way I'd go.