I have a top/bottom kegerator that I made/use for now. Works great and doubles as an extra freezer/fridge, but it also screams "college" and "bachelor" lol. It will probably end up in the garage in the future, there's no reason to sell it since I would only lose
In the future (when I grow up

) I am pursuing the same option you are. You could easily convert any of the "free standing ones" to be shoved under the counter like a dishwasher, then just extend the tower through the countertop. The only thing you have to do is design it so the refrigerated air gets circulated up into the tap tower also.
That being said, I think it depends on where you want it and how much counter space you'll need. If it's a small area, why not just get a free-standing unit then build a cabinet/counter next to it? Or get a wide unit and just use the stainless top as a counter?
Otherwise I might just consult a cabinet company and tell them what you want to do. Ask where they buy their "under counter kegerators" or just get a quote for the whole job. It's nothing new so they should have examples of their work too