How can I optimize latency for LinuxCNC on Raspberry Pi 4B with Debian12?

Does your previous test data above not affect the subsequent use of Mesa or EtherCAT?

Did I fall into a misconception? After the installation of Debian 12 and LinuxCNC, I've spent a significant amount of time dealing with latency and fluctuation issues in the testing software without actually testing it on the machine. If the data shown in the picture doesn't affect subsequent use, then I can proceed confidently to the next step. I might have expressed myself wrongly just now. I will be using GPIO and ethercat in the future. I sincerely apologize.

You are fine.
Following the getting linuxcnc process as you first did gives you a Debian kernel and a fairly old snapshot of Linuxcnc and it will not give you access to the on board gpio due to a bug. That has been fixed but until Coenholio and I started building an image in the last week, you had to compile linuxcnc to get the changes.

But It will work for  ethercat as you don't need gpio then.

Cornholio's build is current, it uses the Raspberry kernel and includes updates that let you get to the gpio and even spi if thats a requirement.
It will be interesting to get your feedback on latency between the two kernels.
If i was using ethercat, I would not bother about gpio and use an ethercat I/O module
In that case, this is a better latency test as it only benchmarks the servo thread.
latency-histogram --nobase --sbins 1000

I don't use a pi with linucnc and I was really asking a question to the group why do we need software stepping on the pi?