Like magic! I set the FL to 120mm ignoring the warning message in Ekos and was able to get similar PA error both in Ekos PA and PHD2 drift alignment.
The routine I followed was to first run PHD2 drift alignment and guide assistant first, which reported an error of 6’5”.
Then I run Ekos PA and before adjusting the knobs it reported an error of 4’5”, a bit of a gap but much better than my previous tries.
Then I adjusted to 0’5” in Ekos and run a second iteration which confirmed the same error practically. I then run PHD2 guiding assistant and got 1’5” error.
So in my case there is something like 1-2 arcminutes of deviation between both, for me enough to use the much faster Ekos PA routine. I was able to confirm it by taking same 5mins pictures with perfect round stars.
So in my case it seems the wrong FL was the error, I hope this helps others.