If I am understanding your setup correctly, it sounds like the I2C is connected via an external cable as shown in your pic so the I2C not coming from the Teensy but rather an external device?
If that is the case,...
You want to cut the small trace that is between the two large pads to isolate the USB power from the VIN power.
Use a sharp X-acto or box knife with a new blade. Angle the blade at about a 45 degree angle and press...
Under normal circumstances, the CPU should not be getting that hot. It would normally just be warm to the touch.
If you are plugging both USB and VIN power in at the same time, besides the diode you already...
As Defragster has pointed out, I have some of the Teensy 4.1 in stock, though I am a little surprised he can see my website at all. ;)
Most of the ones I sell are the value-added 'Fully Loaded versions, i.e. modified...