Skiplagging (taking only part of a one-way itinerary with no checked bags) is pretty well known at this point, and most flyers do it to either hop off at the connecting airport on their itinerary, or fly a different airline to a different destination (which I've done in the past). However, my question is:

What extra risk is there to skiplagging with an airline, and flying an onward ticket _on that same airline_? Say I'm connecting on Frontier in Denver, on like an LAX to DEN to ATL itinerary. I hop off in Denver and switch to a DEN to DTW flight that I booked separately. If I need to use the check-in counter in Denver, would the agent see my DEN to ATL reservation, or not because I already got the tickets for it?

Any insight from anyone comfortable talking about this would be much appreciated. If skiplagging posts aren't appropriate for this forum, feel free to discard this as well...

It seems unlikely that if you go to the counter at DEN as shown in your example and give them the record locator for the new flight, that they would see that you're in the middle of a different itinerary. But if you go up to the counter and just show your ID and they use it to pull up your name, then the agent might see you have two reservations. But I ask, why would you need to go to the check-in counter in DEN in the first place, if you don't have luggage to check? You'd just go to the gate of your new flight and board (assuming you printed your boarding pass at T-24 previously.)
Some of the big boys have more sophisticated computers to detect things like this if you've entered your frequent flyer number in both reservations. From what I've read on FT, they let it go unless you have a habit of doing it repeatedly. I highly doubt Frontier would spot such an action.