I suspect what they'll find when they finally rip out all this equipment is that the new system will be unrepairable without huge long term contracts with the original vendor.
These old mechanical systems have their own problems, but repairability is not one of them. Almost any competent machining shop could duplicate one of the switches in the article.
Boston has one unique feature that makes public-ish ownership of specifications and the hardware running more plausible than other cities... it has a large number of technically-sophisticated potential stewards for such a program who aren't going anywhere: all the colleges and universities.
MIT and Harvard are something like the largest land owners in cambridge and boston... they're not leaving anytime soon, and ideally they have an interest in maintaining relationships with their community. They're invested in the area, and as academic institutions, inclined to support open source initiatives like this (how many of you use the MIT keyserver for your PGP keys?) Imagine a "civic service" initiative where the area universities are stewards of the open source implementation for the city's infrastructure.
Not at all saying you want the T to run on overworked grad student code -- outsource that in a professional RFP -- but if the concern is that technical stewardship might be out of the realm of a municipal infrastructure agency, Boston's academic population could make for an interesting partnership.
Hairbrained stream-of-consciousness idea, but hey, that's what internet forums are for ; )
That's presumably not the kind of operation that can be run in someone's spare time, and exactly the kind of work that graduates from these universities are training towards, and would expect to be well-paid to do.
> if the concern is that technical stewardship might be out of the realm of a municipal infrastructure agency
...then they really must employ someone to do that work. Except perhaps for the tunnels, the signalling system is their most important asset.