2/3 penetration should be ok - as long as it's not so close to the opposing basin wall as to inhibit flow.
Also, if I understand yr second question, you're saying you don't know how the vent and elec cords are sealed to the basin. The lid should have 2 x 2" holes (one for discharge and one for vent) and 1 x 3/4" hole for the cords. The lid should contain rubber grommets/gaskets that make the seal. Your builder might have put a totally sealed lid on it since it was going to lie idle.
You might just need a new lid ($40) from any home center. It comes with all screws and gaskets.