Why ecclesiastical endorsement so important to a military Chaplain?

As a Chaplain, you would be required to administer not only religious support to members of many faiths, but also spiritual wisdom, comfort, and solace.

We expect our line Officers to be able to think critically, solve problems, and write well. We have decided that a good minimum threshold to establish these credentials is a college degree. Because it would take too long to properly vet and analyze for these traits, we have effectively outsourced this analysis.

So, too, for Chaplains. The ecclesiastical endorsement is the Army's way of establishing your suitability for the role of chaplain via outsourcing, because testing, vetting, and analyzing for these traits would take too long (and would be prone to religious bias - whoever is doing the evaluation may downgrade you based on their religion, not yours).

In a nutshell, if you ain't good enough to serve those who pray to your own God, then you definitely ain't good enough to serve the Soldiers who pray to myriad Gods.

It's important because we require a certain set of professional qualifications and/or certification for any specialty in the military that isn't necessarily military-specific. Engineers, doctors, nurses, mental health specialists, the list goes on - every one of those specialties is required to have particular qualifications and certifications before they're allowed to be an officer in that professional area in the US military. Therefore, it is logical that the Chaplain Corps should require the same. We are a professional military, professional standards need to be met.