<Idle|MPos:0.000,0.000,0.000|FS:0,0|WCO:0.000,0.000,0.000>
OK so this is FluidNC telling us that when in the Homed position, it doesn’t see either limit switch active.
And:
<Idle|MPos:0.000,0.000,0.000|FS:0,0|Pn:XY|Ov:100,100,100>
Here, you’re in the not-homed position, but FluidNC is reporting X and Y are triggered (active).
That’s what the Pn:XY means. Specifically, it sees X and Y as triggered.
So, this means you have your limit pin definitions inverted in your config file.
For your X config, change the line above to read as follows (Remove the :low )
motor0:
limit_neg_pin: gpio.36
Similarly, in your Y change this:
motor0:
limit_neg_pin: gpio.39:low
To be this (Again remove the :low ) :
motor0:
limit_neg_pin: gpio.39
Repeat these tests (including sending the ? command)
If the Pn:YX flips and is correct, then try an actual homing sequence.