Ah, thanks for explaining. This seems like a bug in Endpoint. It should be checking the location you added the certificate to for Agent. Can you share the instructions you used to get Agent working and the location you installed the certificate to so we can make sure this works for Endpoint too in a future release.
In the meantime, this thread has instructions to help you get Endpoint connected. In particular, this comment describes how to add the certificate to a place Endponit will currently look.