A number of things. Where does the 600lbs load limit figure come from for the DS? Is that what's on the mandated sticker for newer boats? Because it seems low. I've sailed both DS1 and DSII with substantially higher loads and can't say that the weight was an issue - although with six adults on board eventually you'll run out of room

Weight is not equal weight. If all the weight you are adding is at the transom, you will impact the sailing characteristics of a DS much more negatively than if most or all of that weight is in or near the cuddy. Having a gas outboard permanently mounted in the rear will push down the boat and create drag from a submerged transom. Worse if the outboard is oversized.
When I bring a trolling motor, most of the time I keep it in the cuddy the whole trip, unless I need it to leave the dock or have a bridge passage planned where I know I'll need it. As the motor is light enough, I can mount it while underway. That further reduces the issue from weight at the stern.
Ideally, I would use a 12V NiMH battery, or even a LiIon one. That would save weight - a lot of it: the batteries for a Torqeedo, for example, are light enough to clip onto the motor itself. I'm too cheap for that.
The need for two batteries instead of one is largely reliability for me. I rarely anticipate running down even one; but I have had batteries die without warning. Needing to switch batteries under way is rare enough that I would never dream of installing a switch. I have obtained cables so I can run the motor with the batteries up front. In the past, I would move the active one to just aft of the CB trunk while motoring.
The rest is preference: I put a premium on silent operation, on not having fuel or exhaust fumes, not being able to contaminate the water, an not having to store gas around the house - with the attendant issue of it going bad. And, I admit, I seem to have two left thumbs when it comes to small gas engines: I find that they quickly become unreliable...
I curious about the stress cracking. My understanding is that in the DSII the CB trunk is tied into the lower end of the bulkhead that forms the cuddy opening. That should really stiffen the whole thing, just like the thwarts do in the DS1.