I was concerned about damaging the alternator on the outboard. I have heard/read about damage being done to them if not using a disconnect and I want to know if this was the norm or an anomaly I guess. I fully understand that the trolling motor batteries and the cranking battery are isolated from each other.
Yes, there's risk to boat equipment anytime a charger is attached to a battery that is not isolated from the boat equipment. If you want to hear what an electrical engineer has to say about it, this is your chance.
Will normal operational charging harm any boating or engine equipment (aside from trolling motors we are already instructed to disconnect)? Typically, no. Is doing this a good idea? I say absolutely not.
If the charger circuits were to fail in a nasty destructive way, there is a chance damage could occur. This doesn't happen very often with well-designed chargers as the goal is to design the charger in such a way that failures pose little risk to attached devices.
The greatest risk is from a destructive power surge on the AC power circuit. Example: A lightning strike causes a surge on AC power circuits that eventually connect to the charger. If it's bad enough, it can cause catastrophic damage/failure inside the charger in the blink of an eye. Voltage spikes/surges could reach thousands of volts, passing right on through the charger to anything connected. You can guess what might result.....
It doesn't happen a lot, but it does happen, and when it does, it can be a very bad thing.
There have been cases of extensive damage to engine electronics (wiring, ECM, regulators, etc.) along with everything in the boat
with any connection to a battery being charged. There have been cases of boats experiencing complete loss of all connected electronics. (Being turned "off" is of no consideration for such surges.) Shallow water anchor and hydraulic jackplate power connections not interrupted will put those items at risk also. Surge protectors can help, but I have seen those fused in the event and be rendered ineffective.
I NEVER rig a boat without a main battery cut-off switch. One bad lightning strike from a passing thunderstorm could theoretically do $10,000 in damages, depending on what's rigged on a boat. In fact, the only disconnect switch I use for my own boats is one that disconnects both the + and - terminals of the battery connections.