Hello MJ,
"timeout waiting on completion" usually mean that you have some problem on bus. Do you have something connected to bus?
J8:3 and J8:5 have pullup resistors, so without any external I2C devices it should show you just empty table.
i2c-1 is connected to clock generator chip with I2C address 0x70.
Usually if you don't want to load drivers for your I2C devices or tune clock speed, you need nothing related to I2C in system-top.dts
Best regards
Oleksandr Kiyenko