I think the idea (in the original project) was that the two tracks would be centered in the ROW and additional gravel ballast could be piled on top to raise the elevation by a foot or two.
Looking back on it, though, I can't see any official source that claims Metra ever wanted to raise clearances at every street crossing, as The Urbanophile claimed
in his blog post. The middle section in the "single-track" scheme shows the new bridge with the exact same clearance as the remaining old one.
Certainly some crossings on the UP-North are drastically low, and at these locations Metra may try to raise track elevation. But at Berteau and Sunnyside, they seem content to leave clearances unchanged and put in the strike beams. Berteau is currently 11'8", Sunnyside is 10'10" per the city's master list
The bottom elevation of the new bridges might be a few inches higher than the old ones, and Metra can probably gain a few extra inches by shaving the roadway. That's not enough to bring it to 14'6", though.