As you have discovered, the parasitic draw on the starter battery can be a killer. I measured the draw on my 2016 Sprinter at 50 milliamps. Keeping the starter battery charged will extend its life, as evidenced in my case with the original 2016 battery still going strong at almost 80k miles.
I don't have the dual alternator setup that you have, but my original configuration (since changed) with the Sure Power Separator functioned in much the same way in that the two batteries were isolated and the starter battery only saw a charge when the engine was running. See post #617 in my build thread for my initial solution: https://www.sportsmobileforum.com/fo...-16293-62.html
I see no reason to disconnect the battery while the trickle charger is connected. I didn't in the configuration shown in my post and everything functioned just fine. Are you aware of the master disconnect under the dash adjacent to the accelerator pedal? Your choice of connection location may be influenced by this, depending on which side of the disconnect you want to connect to. Had I not proceeded down the path of replacing the separator with an ACR (read posts 617 to 643 for the full story) I would have made the connection directly at the battery had I chosen to install a hard-wired solution.