The cost estimates presented here for the GLX are from 'official' documents. The cost estimates presented on the GLR/OLB are derived from 'official' documents for similar projects, namely using the proposal to extend the Blue Line from Bowdoin Square into the same rail corridor and to the same end point, West Medford, as the GLX, and the proposal to extend the Blue Line from Bowdoin Square to the Red Line at Charles/MGH Station. These calculations are detailed on page 7 of this site.
The largest margin of error in that process would be for the estimation of costs to take the Blue Line from an underground station at Science Park to run beneath the Charles River and then underground to Lechmere, to include a new underground Lechmere Station. That estimate was one of three adjustments made to the Blue Line to West Medford cost estimate in deriving a like cost for the Orange Line branch to West Medford.
The estimate for the Blue Line segment (under the river) from Science Park to Lechmere might could be reduced by 25%, making it only 50% more than the costs to take the Blue Line from Bowdoin Square up Cambridge Street to the Charles/MGH Station. If so, the estimate for the GLR/OLB would go up by $222,091,200 (87,300,000 x 2.544). The 2.544 is the same increase that occurred in the GLX estimate from 2003 to 2009.
A final point to make here . . .
Let's throw out all of these numbers and say the two proposals costs the same to implement . . . they are the same price! Now, which would you buy if it were your money? If your answer is anything like mine, then show you care about how YOUR/OUR money is spent, let your elected officials know you care, and that they should too!