With regard to
Yes, this is a risk. One way to reduce the risk is to have a MasterShunt in the battery box. This is what we did.
When a MasterShunt is present on the MasterBus, the Alpha Pro regulator looks to get its battery charge info from the MasterShunt. Since the MasterShunt is installed in a vibration-free zone, and adjacent to the batteries, the chances of a damaged or loose wire are minimal.
A secondary way I manage this risk is by feeding a small B&G chart plotter we have on deck with 24V. This Zeus2 chart plotter is set to display its VSUPPLY on its databar at all times. After several years cruising, I've gotten quite used to peeking at that little square from time to time for the current voltage.
A tertiary way is to have a voltage monitor on at all times (an EasyView 5, in our case). We have it highly visible from the companionway; it never sleeps.
We've never yet had an over-voltage event, so those cautions look unnecessary. May it be so always!