Most people cant perceive the difference in sound quality between a low end and high end head unit. THe key to a good sound system is adequate power which typically requires a separate amp, quality speakers and quality wiring.
I'm going to assume the standard sound system just uses what power is available from the head unit which typically isn't much. Looking at the specs on the Jensen its about 20W per channel. I agree you could probably build something your own for less money however if Eclipse upgrades the wiring during manufacturing then it might be worth it. Trying to upgrade the wiring on a fully constructed trailer would be a complete PITA.