Hi,
I think there is zero chance you are going to damage the solar charge controller. It is just going to see a voltage and act accordingly. If the battery is being charge by the alternator, the charge controller will likely see that as a fully charged battery and go into float.
PV panels are hard to damage -- you can short them out indefinitely with no damage. I suppose if you applied a high enough voltage to them the reverse current might damage the panels or protection diodes, but hard to see how the charge controller could ever do this?
Have Midnite Solar Kid charge controller and charging from alternator via an isolation relay since 2014. Have noticed no problems with components or house battery.
Some use a switch to disconnect the house battery from alternator if they have enough solar to charge the house battery under normal circumstances, and only close the switch when solar is not doing the job. I guess this can't hurt, but don't think its really necessary.
Seems like one of the best things about having the house battery on solar charging all the time is that it keeps the house battery fully charged, which is good for life of lead acid batteries.
Gary