Im just guessing since my car didnt have a stock alarm, but is there a fuse for the stock alarm? maybe you could pull the fuse if there is one.
The dealer is right, theres usually 2 horns, one for stock alarm and 1 for regular horn. Maybe the dealer had the 2 mixed up? Try unhooking the bottom horn and leaving the top one in?
Stock alarm is probably only monitoring door opening and hood opening. Maybe the wind is causing it to trip one of the triggers. Maybe disconnect your hood trigger (there should be a clip under the hood trigger) and see if that is what sets off the alarm.
These are just guesses
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