This can indeed be somewhat confusing. Please refer to the "Prewhitening" subsection of the "Details" section in the ARIMA doc.
When y is a response that is being modeled with x as a predictor, pre-whitening of x is done to help identify the form of the transfer function. This form is identified by looking at the cross-correlation of pre-whitened y and pre-whitened x. Once the transfer function form is identified, the pre-whitened series are "essentially" discarded. The model with y and x is fitted with original y and x series (and not their prewhitened versions). There is one issue: when prewhitening is done, the initial parameter estimates could be based on the prewhitened series but these often lead to the same final parameter estimates. This explains the behavior you see.
In summary, the output of
Identify Var=y CrossCorr=x;
does depend on whether x and y are prewhitened but the output of
Estimate p=2 Input=(3$ x);
is essentially independent of prewhitening.
Hope this helps.