If you have two 12 volt batteries and are charging them in parallel, I would check the water "more often" than if you are just charging a single 12 volt battery.
This is just based on my experience but I was maintaining 2 12 volt batteries always in parallel with a 20 watt panel and a Morningstar PWM controller and one battery would always have a lot of water loss. I had even gone through the effort to make sure the wiring was balanced, that did not solve the problem. That is it main reason I now have two 6 volt batteries, I’m basically just charging one single 12 volt battery.
I think you have had this issue in the past and so have I but every charge controller I’ve had experience with takes its power for the control (i.e., the brains) from the battery side - not the panel. So if for some reason the battery gets low, the charger just stops working and no longer charges the batteries. Where I had the problem was leaving the solar panel just sitting in the boat and left it for a few months. The wind blew the panel over so that it barely got any sunlight and when I finally got to the boat, the batteries were something like 9 volts but they seemed to recover OK.
I now have a fixed mount 10 watt solar panel charging the batteries through a morning start PWM controller and it’s been reliable for over a year now. That is also with the boat and batteries getting very hot during the summer (Havasu). I get very little water loss with the single 12 volt battery (composed of two six volt golf cart batteries in series).
Your controller should manage the 100 watt panel just fine, it’s just the two 12 volt batteries always connected together that I would worry about. But that is just based on what happened with my batteries, I could have had one weak battery to begin with.. don’t know.