Well, taking your condition literally, if I lose track of time and keep finding new complexities to my decision that I didn't see before, I could not realize that I "have a tough decision that could take me longer than 3+ minutes to make" after five minutes.
I'm not going to click a stopwatch on myself just because you're too lazy or rude to type a few characters into chat and check if I'm there.
I think quite often (on Dominion Iso) and don't have any problems communicating that to my opponent. The obligation of who figures out how long a turn is going to take should fall on the player taking that turn, not on the player waiting for his opponent to finish.
Honestly, when in doubt, just type "thinking" at the start of your turn. This has the dual benefit of making it more likely that your opponent will ask if you are there if he gets impatient.
Dominion is VERY different. Your standard works much better in Dominion. The outlier-long thinking times are much easier for a player to recognize. Innovation can run into "just 20 more seconds" loops of thinking about new things, so it can be hard to realize how long you've been sitting there.