Do engineers make these decisions though?

Yes.

The way that it works is that the plans for every construction project like this must be stamped by a licensed engineer, or else they cannot legally be built. Then, the construction itself must be supervised by another licensed engineer, to ensure that the as-built condition conforms to the plans or that changes are properly vetted for safety.

Under this fact pattern while engineers are responsible to protest, I would posit the ultimate discioson maker should be held criminally liable first then we can talk about engineers proffesional responsibilities.

That "fact pattern" is false. The ultimate decision maker, the person who should be held criminally liable, is the principal engineer who stamped the plans.

This is what licensing engineers is for!