Uh, when Lex and 125th alone is expected to cost half the proposed budget, yeah, we have a problem.
With the amount they want to spend on that section, you may as well build an immersed tunnel under the (very short) Harlem River and take it to The Hub. And yes, it might be somewhat more expensive, but the overall gains are worth it. Because it guarantees The Bronx two new lines.
Lastly, The Bronx should be world's cheaper to tunnel through. You won't have to do it anywhere near as deep compared to Manhattan. Property values are nothing compared to Manhattan. For all we know, it might cost the same.
But until I see the two options quantified into numbers, the "capitulating to the suburbs" response isn't good enough.