I have an 1820 Action Craft and a 40' Mainship. My wife and I have been spending between 3 weeks and two months a year in the Bahamas every year since 2007. At this point I primarily go over there to bonefish and freedive.
Many, many times I have wanted to tow the skiff over, but I have never done it, though I know lots of people who do it every trip. Counting over and back as two crossings, I have crossed the stream to the Bahamas about 50 times and I am always very, very careful about weather windows. About 20 of those crossings I could have run the skiff over it was so calm. Another twenty would have been OK towing it. Five of them would have been really challenging with a tow. And the last five I am pretty darn sure we would have lost the skiff and possibly put the big boat in trouble as well.
In the end, I have decided it is just not worth it. Instead I have a really good tender (a tricked out 11'6 Highfield classic with a 20hp electric start Merc). I usually use it to get to the flats, then get out and wade. I bring a push pole with me as well and can stand on the yeti box I use as a seat and pole it, but most of the time I wade. It's a good dive platform as well.
Here are my random thoughts.
It's darn near impossible to pole and fish at the same time, so if you don't have another person with you who can pole you are better off wading in most situations. A trolling motor in shallow water will spook bones most of the time.
Bahamian law technically says you can't flats fish without a licensed Bahamian guide on board. Most areas don't enforce that law, but some, notably Andros and Eleuthera, are very serious about it. Wading from a dinghy doesn't stir anyone up, but showing up in a skiff with a poling platform on it will attract lots more attention and could get you in trouble.
My skiff tows pretty well at up to about 8 knots. Above that it gets squirrly.
You will burn more fuel.
If there are three or more of you aboard that are good boat handlers it will be easier. If just two, like us, it means you are singlehanding into docks and anchoring while your mate runs the skiff.
A 17' Hewes would be a great Bahamas platform but it is too big to put on anything under 70'.
My buddy has a 62' Princess with a 14' Marsh Skiff on the hydraulic swim platform. Last year my brother and I helped him deliver the boat to the Bahamas (his first trip with the skiff) and "guided" him on some of my favorite flats. We caught a ton of bones, more than I do wading, but it was a lot of work having two real boats to deal with. We went out through Ft. Pierce inlet on the way over on an outgoing tide with standing 6' waves, it was rougher than forecast. Despite being tied down with four 2" ratchet straps the skiff slipped sideways and tore one of the pad eyes out of the platform. It also filled halfway up with water. While we were over there the jackplate broke with the plate raised all the way up and it had other issues as well. I ended up doing a LOT of mechanical repairs.
A microskiff like my buddies might fit on a bigger trawler. Microskiffs work great for bonefishing, but are not great for diving (too tippy) or getting groceries, bringing the dog to the beach etc.
Hope that helps!
Doug