The KISS solution is to do away with resistance to nonmagical attacks entirely, except when it is highly thematic. For example, werewolves should be weak to silver, and horcruxes can have a small list of weaknesses.

But does every high CR monster need this? Does it add anything to the narrative? It could, with a proper DM and a game where these creatures are major threats, not encounter #2...but this rarely manifests ime. In practice, the DM has to halve a bunch of numbers for no good reason.