I have a similar situation in my Toyota PU. My alarm is a passively arming one so that 45 sec after I open and close the door the alarm arms. To enter I have to turn the key past ACC to START w/in 15 sec. Typically, I'm not ready to start the engine in that time, so I end up getting part way through a boot by the time I get ready to start the engine--though naughty me, I don't wait for the first boot to finish and just crank her over which initiates the second boot. I agree it does take too long, but I don't think it is looking for the tuner that is causing the delay.
More troubling for me (and I admit to not searching the database yet) is this: Sometimes, not always, when I turn ACC power on momentarily, the player boots up and then stays on playing--even when the key has been removed! This happens when I enter the armed vehicle and just want to disable the alarm by turning the key to START and then back off again (Toyotas have to have the clutch down to enable the starter so it safe to do w/o being in the seat...) ACC operation works as I would normally expect if I allow the boot to finish. The other morning I did this only to find the player meandering through the playlist when I got home that evening without me hearing the tracks--ARGH.
Fortunately, the player is slaved into the head unit so only the empeg was on and I still had battery life left.