I’d like to start from the reference point step, I think this is different to what you are looking for, Or what is the goal behind the selection of reference point.
In here our colleague has selected a high coherent pixel and then according to the value of coherence result, he considered as a reference threshold of the coherence and hence of the deformation.
This is easy to apply, once you have created the coherence product, you could open the band math, and apply the following statement condition to create the mask, for example,
IF coherence >= 0.35 Then 1 ELSE 0
The result of aforementioned statement is a mask of only the coherence = 0.35 and higher , the other will be 0, this mask named coherence multiply by the original coherence map, will result only an interferogram of the selected coherence,
Please keep in mind, there is a difference between what is mentioned in this post and the reality behind the selection of the reference point.
An important thing it is worth mentioning here to give you an entire answer concerning the reference point, Please take a look at the following post,