are you talking about an MPPT solar charge controller? It should be running the panels at their maximum power point for their temperature, independent of battery temperature, provided the batteries can sink the power. If the batteries were in the absorption (current limit) phase, then the controller might be backing off based on battery voltage and temperature. In that case, sensing cooler temps would do as you say. Generally speaking, the IV characteristic of the raw solar cell output is at non-linear curve down and to the right: more voltage means less current with a distinct knee at the maximum power point, and all curves shifting down as solar cell temperature rises.

The battery temp sense really should be attached to one of the battery terminals (usually specified as the negative one) as it gives the best reading of internal temps. Battery temp sense is not so important with flooded cells, but very important with gel or AGM.