It can be the 4.19 kernel in debian 10 that perform must better than kernel 6.1 in debian 12.
When I was working on my own EtherCAT board a year ago I had some timing issues
and compared the network adapters and linux kernel version in the computers I had around.
linux 4.19 performed better especially with Intel adapters.
Often I had to go up to 2 millisecond servo loop to get acceptable performance.
This is just to show that there are several factors that influence the timing performance
and when you compare with debian 12 and 10, the kernel version is definitely a factor.
The network adapter is another. If you have a Realtek network adapter and have tried
all settings that rodw lay out in his document and you have a free PCI-e slot in the computer
you can try with a cheap Intel network adapter. I210, I225, I226 for example. I have had good luck with them.
Not sure how that comes in here, but you should nevertheless bring down the normal real-time jitter
to single digits, less than +- 10 microseconds, the one you check with latency-histogram.
The WARNING you get, and the delay, is a nuisance more than a real problem. The Ethercat master
will synchronize the time of clients, it just takes longer than 5 seconds. Googling around for this issue
one can see that this issue has been there for more than 10 years and one way to get rid of the warning
is to just increase the 5000 ms level when compiling the ethercat master yourself. You will get the delay though
Here is a short article on DC clock synchronization
www.acontis.com/en/dcm.html