Hi @alejandro_e ,
Thank you for the complete explanation, now I think I can ask/discuss the test/data a bit better.
1_ Relating to that GPIO4 pin, in the configuration you have it with both input and output drivers active. Why doesn't attaching a wire to +3.3V supply cause excessive current draw on that pin assuming the output buffer is set for logic 0.

This is a 3.3V IO (port voltage VDD_IO_G is only allowed to be 3.3V). I'm not sure what the output driver will do since the SRE value of 000b selected is a reserved value. But typical output resistance of the 3.3V output buffer is

So it would seem the I = V/R = 3.3 / 50 Ohms = ~66mA could damage an IO...but maybe there is some protection there or I'm not understanding why the output buffer being enabled for the pin you are driving from the 3.3V supply might not be bad.
You mentioned selecting input/output for the direction in the configuration, but I don't see any pin setting in the code that reflects that other than both input and output buffers are enabled like he pin configuration tool also shows.
Question is why driving the pin in this configuration (output buffer enable) is OK?
2_ For both the rising edge and falling edge plots, I can maybe understand the long rise/fall time of Ch1 since it is being switched by your wire (inductance, etc.). But I'm confused by the equivalent and slow rise time of the GPIO48 signal generated by the MCU. GPIO48's (Probe Channel 2) rise/fall time is on the order of 10us, this would limit the clock frequency on that pin to 50kHz (1/(10us rise + 10 us fall); that's not even enough to support 115.2k baud serial communications?...just seems really slow.
Keep in mind that latency core to IO should have nothing to do with how fast the IO line transitions when the data eventually reaches the port buffer.
Is there something that could be loading the pin or causing this?
3) The input high level voltage threshold has a min of 0.7 * VDD_IO = 0.7 * 3.3V = 2.31V.

Looking at the 2 rising edge plots, it seems GPIO48 output seems to start rising at almost the same time as the input GPIO4, even thought the change should not be detected until the signal is at least above the 2.31V value.

4_ From the same Table 10 from the datasheet the maximum Input low level threshold voltage is 0.3 * VDD_IO = 0.3 * 3.3V = 0.99V.
If we assume the GPIO4 signal input buffer transitioned from 1 to 0 somewhere between 0.99V and 0V then its really hard to estimate a latency because GPIO48 starts to fall within this same window.

Overall Comments:
The rise/fall times for GPIO48 seem unexpectedly long, basically something seems wrong to me. The slow rise/fall time on the input GPIO4 make it hard to know when the input transitioned with any time certainty. The fact that GPIO48 started rising before GPIO4 was even close to a reasonable threshold voltage is very confusing.
I would think if there was a lot of bounce in contacting the wire to GPIO4 it would be in the plots, so don't think that's it.
Could the scope have some low pass filter setting turned on?
Keep in mind I'm trying to determine latency on the order 10's to 100ns.
I would suggest triggering GPIO4 from another GPIO output to have a fast transition signal for CH1 probe, but the fact the GPIO48 looks slow means there is more going on.
Please let me know your thoughts.