I think that it's dangerous to assume that Ysayle's group was "different" in the ways that you claim. While there are clearly factions among the heretics (evidenced in part by the fact that there are still heretical hold-outs even though most heretics have now surrendered), Ysayle clearly considered herself to be an ally of Nidhogg when her crew paved the way for the assault on the Steps of Faith. It wasn't until she witnessed the indiscriminate savagery of the attack against civilian, military, and clergy alike that her convictions were shaken and she began to wonder whether assisting Niddy was really the right thing to do. Her Echo had given her the knowledge that the Church of Ishgard was in the wrong - but it wasn't until then that she considered the fact that the dragons could ALSO be in the wrong, and that helping them to win the war might not solve things the way she thought it would.
Claiming her group as being non-transformative seems wrong, as well, as the quest leading up to your meeting with her explicitly involves a fight against a group of heretics who transform during the fight in order to protect Ysayle from you. They are clearly her people, and possibly even her personal guard. It is implied, too, that Ysayle is considered a leader figure among heretics in general, not just a small group of them. Even if not all factions obey her directly, she seems to be something of a prophet to them.
On the topic of aevis, note that Bahamut had a couple diresaurs (another result of Elezen transformation) assisting him in Coil 13, and the Allagan/Meracydia conflict LONG predates the whole Ratatoskr drama. There are apparently other methods to transform people into dragons than transforming Elezen descended from the Knights Four, so there could well have been aevis, as well. What those methods might be is currently a mystery.


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