Disclaimer: I do not own a model 3 or Y but enjoy collecting information about it. If you can get the charge port open, then you can charge the car and it will then also charge your dead 12 volt battery. Should be the same with the Y
In my Model X and the Model S, if the high voltage battery and 12 volt battery are both dead, it is hard to get the charge port open and so you have to open the frunk, find the hot plug to the 12 volt battery and then charge the 12 volt battery a little until the car wakes up and you can open the port.
Do me a favor. Supposedly if the 12 volt battery is dead on the model 3 or Y, you can pop the small port open on the left front bumper (rotates with the help of a plastic pry tool, rotates from 8 o'clock up to 2 o'clock) and applying a small current to the positive and negative cables attached (9 volt battery, or 12 volt jumper), it will pop the frunk and you can then pull the plastic cover off in the back of the frunk to get to the fireman's harness disconnect and your fuse box and the hot plug to the 12 volt battery inside. You can then jumper the dead 12 volt battery (ground to the metal chassis) and get the electronics going again. Can you try this emergency procedure and see if you can find the 12 volt hot plug in the fuse box? You don't need to actually charge it, just see if you can find it!