Yeah, all of that. MARAD has some short-sea shipping studies and they queried industries on what the problems are (http://www.marad.dot.gov/ships-and-shipping/dot-maritime-administration-americas-marine-highway-program/americas-marine-highway-program-reference-library/):
"Noted that the principal obstacles to effective development of short-sea shipping services were the cost of domestically built cargo vessels, high stevedoring costs in U.S. ports, and manning levels for self-propelled vessels engaged in domestic commerce, as well as the cost to shippers of Harbor Maintenance Tax (HMT) assessed on domestic shipments. "
So, in comparison between tug/barge and coastal self-propelled, obviously much of the costs above are comparable between the two for taxes, stevedoring, so the cheaper option relies on the treatment of tug/barge versus coastal freighter for regulatory purposes. In such comparison, US manning laws are the big difference. For example, that Damen coastal freighter you link--approx 1767 gross tons, assume that's ITC, maybe you could regulatory tonnage it down significantly, by the ballast tanks being excluded, a few tonnage openings, not sure but doesn't seem realistic to get it below 1000 gross register tons (maybe a nav arch could comment) but even if you could, it seems highly impossible to get it below 200, or 100 (which would be the ultimate for cutting down impact of US laws on manning). So, let's say over 1000 GRT... The laws call for a master, 3 mates, chief engineer, probably two more licensed engineers, 2 ABs, 1 OS, maybe an engine rating (total crew 10, maybe 11). If you promise not to go over 400 miles or get it below 1000 GRT, can take off 1 mate, but now your market area maybe limited. Tug and barge, presume a tug capable of pushing an equivalent cargo capacity barge would be much lower tonnage, probably just need a master and mate, maybe another mate if voyages will be over 600 miles, engineers would be variable--tonnage would matter. Depending on how much regulatory tonnage a tug would be able to achieve, much less manning possibly down as low as four on some voyages.
Add in the lack of coast guard inspection and regulatory requirements (e.g. accomodations, lifesaving, more bodies = more lifesaving equip of course, and maintenance) not surprisingly, the tug and barge has been (and will remain) a much cheaper operation.