Hey there, you ... monkeys! Just wanna ask a question about that run category, why doesn't the run include the monkeys we can get with the codes once we finish the game?

The all monkeys category would best be described as beating specter the second time. Which only requires the monkeys in the levels. The category was originally called Any%2 but by popular demand was changed to All Monkeys, as that's the general idea of the category. In short, the unlockable monkeys are not required to beat specter the second time.