Despite their ratings being the same, the batteries will be slightly different so there's some benefit to independently charging them. My initial question was in fact, will the solar cause the relay to combine the batteries. These devices are voltage triggered after all. When I install the solar I will likely connect a relay to the negative line on the relay. This way, the relay will only be active when the battery switch is on or if I can find an independent output on the alternator, when the engine is running
The ACR connects the battery when one side of it has a specific voltage applied to it (see linked article for a much better explanation). When there is sufficient solar output and the controller raises the voltage to that level, the combiner will close and the batteries will be connected.
It is correct that batteries will have different charge acceptance rates depending on different ages and conditions, however the charge acceptance is current, not voltage based. The amount of amps a FLA battery can accept is determined by the battery and not the controller, if the controller is set to provide 14.5v in the bulk stage, it will provide as many amps as it can at 14.5v. If one battery can accept more amps than the other, it will accept more than the other battery.
On LA batteries the internal resistance of the batteries will determine how the available amps are divided, the battery with the lower internal resistance will accept more.
In real life, a dedicated start battery will seldom if ever be deeply discharged as the number of ah needed to start is remarkably low, on the order of 1 or 2 ah per start. As a result, it is recharged quickly and the internal resistance goes up, reducing the number of amps it can accept. If the start battery can only accept 1 amp and the controller can provide 5 amps, then the remaining 4 amps will go to the house batteries. There is no advantage, and perhaps some disadvantages to turning the ACR off and on or by passing it under certain circumstances, with one exception* that has nothing to do with distributing power from solar panels.
Making Sense of the ACR WARNING: ACR's are not for use with LiFePO4 Batteries! What is an ACR? An ACR is nothing more than a fully automatic, voltage triggered, BOTH/PARALLEL switch that closes when charging voltage is present and opens
marinehowto.com
*The one exception is while starting the engine. When the starter is first engaged the current, the voltage on the start battery can drop causing the a power surge through the ACR that can damage the ACR, that's why there is a start interrupt circuit to protect the ACR.