Hi,
The fact that at various times, various reputable manufacturers have used each system shows that both systems work.
Personally, if I had found a suitable boat with ropes, I would have bought it. This is because I find it easier to climb back on board using ropes rather than a fixed handle. I do a lot of swimming and snorkelling from the boat.
However, at the time, the best option for me in terms of size, price, availability, was one with handles. It works perfectly OK, but climbing back on board is a bit more of an effort.
In terms of sitting on the side tubes, ropes will give you more choice of position, but the handle will feel a bit more secure.
You may be overthinking this. Either will work.
Rules of SIBs:
On the water, the bigger boat is usually better.
For the rest of the time, the smaller boat is more convenient to store and transport.
You don't spend as much time going flat out fast as you expect, and fun can be had with a smaller, lighter engine.
Fat tubes give a dryer ride.
The number of opinions is N+1 where N is the number of enthusiasts you ask.