Hi B.,
This is one of those times that I would definitely agree with you and the doc over your mother. While you certainly can get a second opinion before going to the endo, if the doc sees the weight loss your describing then it will probably come out with the same result - referral. The reason I say that is because your doc is probably erring on the side of caution and trying to rule out any medical reasons for your son's weight loss, especially since there are no other issues.
My sister sees an endocrinologist regularly since she was diagnosed with type 1 diabetes at 9. Going to her appointments with my mom when we were kids are about my only exposure to them.
They will probably get some blood and collect urine some how, and what I would do when you schedule the appointment is ask to talk to one of the nurses. Although the nurse hasn't seen your son's chart, if you describe the reasons for your referral I'm she he/she will be able to tell you how they handle the collection process for young children, and what the appointment will be like. Children's Specialty Healthcare automatically sends this info to you in the mail when they send you the new patient packet.
When my son had to see a orthopedist and get x-rays of his spine, I did exactly what I am suggesting to you, and they were very helpful. They also let me talk to one of the x-ray techs because I was concerned about getting how they could get accurate x-rays of a squirmy baby.
On a side note, I am a nutrition major at the U of M right now, and we are going over life cycle nutrition - covering the toddler ages. The general rule is that weight loss is not a good thing. Although Sharon talked about how her child changed percentiles on the growth chart, a change in percentile is different from actual weight loss. Most the time if it does occur (the weight loss), it's only because the child is so busy and not paying attention to hunger cues. An emphasis just gets placed on getting the child to eat more and then the weight comes back. On a rare case, it's a sign that there is a endocrine or metabolic problem that needs to be addressed, and that's what is prompting your doc for the referral now. Usually an endocrine or metabolic issue can be compensated for once it's diagnosed. I could go on here, so I'm just gonna stop (LOL!) because it's more info than you need. Either way, I hope things work out well and that your son starts gaining weight again soon!