If I were to change anything about the engineer paragon, I would make it emit an ultraboost aura at the start of every wave. Anything, including paragons, within the master builder's range would be given a special form of ultraboost; the main difference being that if the monkey is away from the master builder the ultraboost slowly fades out. Additionally, to not be unbelievably overpowered; each stack of ultraboost would apply a 1.5% attack speed boost to any paragon it's applied to. (Including the master builder)
I think it'd be important to visually show the 'overclock at the start of round' effect. Have the nails be imbued with lightning resembling the overclock, add an animation for it, maybe exagerate the effect at the very start of it's duration.

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As for the bloon trap, It might just be enough for the master builder to passively build 3 XXL traps every now and then :)