I realize that Caesar analysis is not perfect for HDPE piping. I am trying to use Cesar to get a general idea of the stresses we will see during line installation. I am wondering, is it useful to perform flange analysis for HDPE piping? No gasket is needed because of the malleable nature of the HDPE flanges. Also the flanges would not act as rigid bodies.

Any advice?

My only advice is to avoid getting involved with the stress analysis of any flange. It's a lot more trouble than enlightenment.

You are right about all of the rest that you say - HDPE pipe is generally not worth the truoble to analyze with software - just get the hoop stress right and use a crude method to size expansion loops. It's a very forgiving material.