My basic premise in everything that I do is to not leave myself traps to fall into. If everything is manually operated and I forget to do one of them, then that's a "trap." Some things I only want to operate manually, but there are things that should happen without my oversight. Like battery charging.
Diode bridge isolators are a nice idea with one large pitfall. There is a voltage penalty for crossing the bridge. Unless the charging system's regulator is adjusted to offset this loss the batteries will never get fully charged. I experienced this in an early dual battery system that I had in my '66 Econoline van. The batteries always were down, and at the time I didn't understand the problem.
I see the VSR/ACR's as an automated version of the simple continuous duty solenoid method. They do not combine the batteries until the starting battery has reached a set level of charge. So they're like a person sitting there watching the voltage level of the starting battery and then throwing the switch when it has reached some given voltage level, rather than simply coming on when the ignition is turned on.
For me, having a manual battery combiner switch under the hood instead of remoted to the dash means that I'm much less likely to forget that the batteries are combined and run down both of them. Some folks want that control on their dash, but for me that is a recipe for eventual disaster as that switch will get bumped to some unintended setting and not noticed until there's a problem.
Charge regulators, whether internal or external, vary the excitation voltage of the alternator's field to control voltage output. There can only be one of that style of regulator per alternator.
When paired, thru any method that does not cause a voltage difference between the batteries, the regulator will 'see' both the combined voltage of both batteries and not over-charge either battery. If there is a voltage drop or resistance of any significance in the cables to a battery, then that battery will look artificially low to the regulator, and it will attempt to charge it up to the correct voltage. So classically over-charging of only one of several batteries is not the fault of the regulator, but of the cabling and related hardware.