Perpetual changes should be Layer 1 or Layer 3 continuous effects, not effects applied in the layer corresponding to the type of change
Perpetual changes are supposed to be permanent changes to the card itself. It thus makes sense that they would be applied as layer 3 changes to the text of the card or even layer 1 changes to underlying card. Instead, the game implements them as if they were a continuous effect from some external source, like an invisible enchantment in play or a counter that follows the card through all zones. Because of this, it applies perpetual changes in the layer corresponding to the specific nature of the change, which produces very unintuitive results. For example, if you Witness Protection or Frogify a creature who has a perpetual power/toughness bonus, the bonus is applied on top of those effects despite the perpetual change being a change to the underlying card that intuitively should be overwritten by the card losing all abilities and becoming a 1/1. Please consider changing this implementation.