Using Rv4 the chaos dragon seems to deal 110 armor ignoring damage per attack pretty much oneshotting a fully equipped player with 80 health and full armor. Is that intended? Player was wearing modular armour from the mod named like it.

That sounds about rite. Your best bet is wyvern or better yet draconic armor.

Do you do a special check against the player's armor and if it isn't wyvern or draconic it oneshots them?

No it just dose a tone of damage that bypasses armor. The wyvern and draconic armor have the ability to protect against damage that would normally bypass armor. Wyvern only blocks 50% so it may still be a one shot but draconic blocks 100%

Pro tip: Do not use last stand on draconic armor. When you run out of levels you will die even though the draqconic armor should protect you.