This is a poor design for a General Purpose development board.
I can see why, but WHY!?
The 2.2K pullups on SDA/SCL are appropriate for most, not all, I2C bus networks.
In an I2C bus you usually want the pullups closer to the I2C devices, not the controller. However this, as you have found, cripples GPIO13 and GPIO16 for almost any other use. If you are comfortable with a soldering iron, or if you have access to a rework tool, I would remove R31 and R35. This is simply the wrong place for I2C bus pullup resistors.
Alternately if you use an NPN transistor to invert the PIR output then you can use it on GPIO13 (or GPIO16). Be sure to put inverted: True
into your device YAML.
I was wrong in an above post where I said the PIR module is an active high/low output. It is only an active high. Putting the transistor in the PIR output will invert it to an active low.