Photovoltaic mounting systems that form chemical flashings are provided herein. Such mounting systems can include a mounting plate adapted to interface with an off-the-shelf mounting puck so as to allow mounting of the puck on the roof surface without use of traditional roof flashing and/or modification of shingles of the roof surface. Such mounting plates can include a top surface adapted to interface with the puck and a bottom surface that defines a cavity between the mounting plate and the puck in which to form the chemical flashing by injecting a flowable sealant into the cavity via an inlet of the mounting plate that remains accessible from outside the puck during mounting. Such mounting plates can further include features for orienting the plate, directing runoff away from any sealed roof penetrations and filling of the cavity with flowable sealant.