They have been using them for years without issue. You just need to make sure your lith battery is rated for use as a starting battery with the BMS needed, not all are.
You also need a charger with at the minimum an AGM setting for charging. Ionic has one of the better batteries for this, but there are many others now. Relion is another main player.
There are also now many other lower priced options out there.
Technically Mercury is the only one approving them yet, but they also are the only outboard manufacture involved with a lith battery manufacture. Mercury’s and Yamahas have the same basic charging system.
Even before Mercury approved them, you could order out a Ranger walleye boat, from the factory, with not only lith trolling motor batteries, but also a lith starting battery. Go figure.
Go on Bass boat central and you will find the bass guys have been running the lith batteries for years without issue. The only real problems that have been shown are with having the correct onboard charger, using a cheap battery with questionable BMS, or those that have powerpole charging systems, but I think they are slowly figuring that out.
Your better lith batteries have designed their BMS protections to be fully compatible. It is a never changing game though with the newer engines having stronger and stronger charging systems in that they have to keep tweeking the BMS to be able to handle this increased charging rates. I think the future will be a BMS that can be continually upgraded by bluetooth.
Edit, I forgot to add there is one other actual issue, and that is cold temps. If you are one that fishes in cold weather, below freezing, you will have an issue with some lith batteries when charging, and when your engine fires up as it is trying to charge the battery. They don’t like being charged below about 28 deg or so and will shutdown if not designed for it. Your better batteries have options now with built in heaters, and BMS systems where if trying to charge or starting your engine, it will automatically sense the temperature, turn on the battery heater, and not allow any charging till the battery warms up to above freezing. This probably is the one thing that still bothers Yamaha, but there are more and more batteries available now with these heaters and BMS for that. So if you fish when its below freezing in the morning, you need a battery designed for that.
Alot of people don’t realize that with an electric car, there actually are the same issues with cold temperatures. They actually have heaters in them that automatically heat the batteries in cold weather. So you park your car at night and it says say you have 150 miles range left, but you get up in the morning and you only have 100 miles range left, thats because the battery heater ran most of the night.