When the collector runs for a baseline against an EPMDocument I have to select the configuration As Stored after the initial population. I was looking for a preference to set so that the initial run for the baseline is for As Stored, but do not see such a preference. This is on Windchill PDMLink 9.1.
We are currently using 10.1 and there isn't a preference for this setting for baselines. Only for the workspace preferences can you set a collector default which has only 2 options anyways, the default which is latest or the other preference of as stored.
So answer is no, there is no preference to change the collector default for baselines.