If custody is not already being shared equally to some degree and the evaluation takes more than six months or so to complete, the judge will often ignore the report, citing the "status quo" and "stability" factors as reasons for not altering the current custody arrangements.
What this means is that if one parent has temporary custody and works to delay or slow down the evaluation, they will more than likely retain custody regardless of the recommendations in the evaluators report. Attorneys know this, and they'll use delays to their advantage. It's unethical, but it works, so they do it. This is another reason to vigorously insist on some sort of shared parenting during the separation or evaluation period.