Checked luggage is searched by TSA in the states and when it arrives in Belize the bags are not searched until you pick them up. You are standing right there when they go through your bags. When you give them to Tropic or Maya your bags sit around "out the back" for an hour or so.
Whenever possible I always carry my electronics. And customs rarely goes through hand luggage (handbags, knapsacks etc.)
I wouldn't say it is impossible for Belize customs to steal the phone, but I would say that this would be quite unlikely since you are standing right there when they touch and open and close your bags.
Over the years I have lost a number of items from my checked bags at the Miami airport.