Here is a suggested heuristic for deciding whether an effect is magical in nature:
- Direct damage spells/abilites are decided based on damage type. Elemental or arcane damage implies magic, physical damage implies non-magic. Thus, hurl boulder, crushing blow, deadly bite ignore magic immunity, while static blast does not, regardless of the implementation details.
- Non-damage spells/abilities are always considered magical. Is there a non-damage ability in the game that can't be explained by magic? Tame comes the closest. Stun? I guess you might need to explicitly label some non-damage spells/abilities as physical.
I guess what I am getting at is that magic immunity and physical immunity should never cause surprises for a player unfamiliar with the internal details of the engine. When I see a magic-immune creature being zapped by lightning from a distance, I might understand why it is happening, but still a bell goes off in my head telling me that something isn't right.
At the same time, it is hard to imagine how an ophidian could be "immune" to a huge rock hitting it on the head, crystal-infused scales or not. That the rock was created by magic isn't relevant. I guess one explanation could be that the rock isn't actually there, and hurl boulder is a purely psychological attack, however name and animation of the spell do not convey that feeling. On the other hand, such an explanation would feel right at home for spells like imprison, phantom fist, or arcane sword (the latter two don't exist in FE, just examples of wording the spell name to suggest a non-physical damage type; of course, the actual damage type dealt by the spell should reflect that as well).