If your logic board had a VDD_MAIN short, it would not boot at all so clearly there is an issue with your measurements.
The issue here is that you have a water damaged device. When a logic board has had enough water damage to cause issues with booting, it usually already has “too much” damage to make it reliable. If you can get the data off, you should be thankful.
Now if you want to keep working on this specific issue (charging), consider that the charge port, Tristar, Tigris and PMIC are all involved in the charge circuit and that’s where you need to focus your energy. Start probing and report back with your findings.