Personally I am fine with both approaches as they produce different results and can both be enjoyable for different reasons. When NPCs are built with different rules, that can be very good for things like allowing the GM to go more with being creative for the purposes of making adventures, it can also be easier to prepare if NPCs are not as bogged down by the same character creation method as PCs (presuming that method is itself a little involved). It just frees you up a bit on the GM side to play the world. On the other hand, there is fun in games where PCs and NPCs play by the same rules, especially if you are leaning into the game side of things. For instance, for horror, I tend to prefer systems where players characters and NPCS have different rules. But for my kung fu campaigns, where the fun is in competing against other martial heroes, I like them to follow the same rules.