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Re: Are dinosaurs really reptiles?

1) If we found vague impressions in a "stem-scutellate", could we
really be sure they were homologous?

They wouldn't need to be vague. Or even to be impressions, as opposed to carbonized organic matter.

2) Just because it might be preserved doesn't mean that most fossils
preserve it.

Of course most don't.

3) Isn't there some osteological character that suggests the presence
of an amniotic sac in embryos? I can't quite recall what it is at the
moment, but I'm sure I've heard of something along those lines.

I haven't. All I've read is that herbivory (as in diadectids) requires close association between hatchlings and adults and thus the amniotic egg so that the gut bacteria can be passed on, but that's simply wrong -- *Siren* is mostly herbivorous and even a hindgut fermenter, and that's an aquatic salamander that probably has external fertilization.

4) "Apo-Scutellata" would be available for the apomorphy-based clade, anyway.

Yes, but this presupposes the Pan- "convention", which very few people have actually convened upon...