I don't think the 2000's era Mainship 400 is the best sea boat out there, but I wouldn't say it is below average. Our 400 is far, far more stable than our old Gulfstar 36, and I'd venture it's more stable than the older Marine Traders etc. of that class as well. I've fished on a few Sportfish (most notably a 40 Ocean) in sloppy weather and at trolling speeds they roll about the same as our boat.
Big following seas require some athletic steering in a 400, it doesn't love that point of sail.
An advantage of the twin engine is that you can bump up to 3000 RPM and bang through seas in the 3 to 5 range rather than slogging and rolling through them at 8 knots for twice the time. That's the main reason we bought this boat.
I think the build quality of the 2000's era mainships is decent, they used good mechanicals (engines, heads, AC's etc.) and improved a lot of things over the earlier 390s. There are better built boats out there, but at a higher price tag.
I would never go straight from NC to the Bahamas in a 400 though. I wouldn't do that in any boat short of a 55 foot plus boat with enough range and power to do it at 15 to 20 knots (fighting the stream) to shorten the window. Frankly, doing the trip that way would be kind of dumb, and not all that much faster than working your way down to FL and crossing over.
10 foot seas in the Stream would be miserable in most boats discussed on this forum. Any skipper with an ounce of sense would avoid that situation.