45-50 years comes from the fact that that's how old the R46's will be when they retire, and that's how old the R32's would've been retired at had the R44's not completely crapped out. And again, both of those cars were around during the bad old days of deferred maintenance; the R68/A's were not. I honestly think the R68/A's could even last for 55 years of reliable service. The R32's are 54 now, and will be closer to 60 when they retire. And while their MBDF is the lowest, it isn't THAT bad considering their age. Not to mention it's really the A/C units that are the biggest problems. It bears repeating, the R68/A's were, and will continue to be, well maintained throughout their life, unlike the R32's and R46's.
And why are you looking to the Port Authority, one of the most wasteful and corrupt public agencies in existence, as a good example of an agency properly spending public money? Have you seen their $3 Billion dollar subway station? Do you not remember how inept they were at finally rebuilding the WTC? Not that I even agree with the decision to prematurely retire the PA4's, but at least there were only 95 of them, and doing so allowed them to have a completely uniform fleet, which they needed for CBTC anyway. Apples to oranges.
Our fleet is already pretty uniform. The R160 order replaced 7 car classes (Most R32's, R38, R40, R40M, R42, R44) with 1 - that's VERY good in terms of uniformity. The R142/A's replaced 8 car classes (R26, R28, R29, R33, R33 WF, R36, R36 WF) with 1, which, again, is VERY good. And 625 IS a lot of cars in the absolute sense, and ~10% IS a lot. You're also not considering the fact that they're 75 feet, so they're really equivalent to 781.25 60 footers ((625 ÷ 8) x 10) = 781.25). Furthermore, they'll probably want to expand the fleet with the R68/A's replacements, so I wouldn't be surprised if the R68/A replacement order is closer to 900 cars.
I also think you're overstating how much it would cost to maintain them for another 15 years. Comparing SMEE train technology to the original 1930's IND signaling is apples to oranges. At MOST it would be in the tens of millions over the course of 15 years, probably a lot less. Those Billions for the capital budget would be much better spent on much needed system maintenance and expansion. Also, speaking of technology, I'm pretty sure only a small portion of the R211's are going to have open gangways - this is a very important technology. If the initial open gangway R211T set goes well initially, we'll get at most 650 of them, which would be about a 3rd of the entire order - not bad. But if it doesn't go well initially the MTA gets to test it out for 10 or so years and work out the kinks, we could end up having an entire 800+ car order with open gangways - a very important feature for our ever increasingly crowded subway cars. And in those 15 years or so extra, maybe even better technology will come along for the R68/A replacements. It'll also give sometime for the MTA to asses it's ever changing future needs, so it'll give them a chance to have more flexibility. So I actually think you have it the completely opposite way - your idea is penny wise pound foolish (lets spend a lot of money to save a little money). And evidently the MTA agrees with me considering there are no plans to replace the R68/A's with the R211's.