I am replacing the am/fm radio in my boat. The old radio was installed after the Perko switch so everytime you shut the batteries off the radio lost all of it's memory (current time and station presets).
The new radio has a yellow wire designed to connect directly to the battery which only draws enough power to keep its programmed memory. Would you recommend by-passing the Perko switch and connect the yellow wire directly to the battery or at the risk of draining the battery during low use periods don't mess with it.
I had the same question as you do when I installed mine, and ended up wiring it so the battery switch would turn off all power to the radio.
It's not a big deal for me because I don't save radio stations on my (boat) radio since it's almost only used with the MP3 player input jack.
I've got a stereo with a blinking light in the ski boat. It sits for 6 months in the winter, battery voltage doesn't change a bit. If you are draining batteries, I might look for a short or something. Some head units may draw more though I guess.