For the trolling motor, I don't see a downside, other than the initial cost.
For a cranking battery, and to run all your accessories......I think the jury is still out. Outboard charging systems have always been persnickety, and they still are. The way that lithium batteries charge makes me wonder how well the stator/alternator is going to be able to stay cooled off. With lithium batteries the voltage regulator is not going to have the regular cool down cycles like they do with lead acid batteries. Those batteries will take every bit of amperage the charging system can put out, right up until the point that they are fully charged. So if the battery is run down pretty good, and you have a long run to make, I can visualize that outboard charging system totally melting down.
I may be wrong, but we'll see. Surely they have tested it and determined it is safe, but I'm gonna wait and see before I personally take the chance with it.