So recapture the transit costs through a
Land Value Tax (taxing solely the value of the land, not improvements).
Tax the land at high rate designed to recover the value that transit adds to "location, location, location" while at the same time taxing improvements within the TOD TIF district at a lower rate (imagine near-zero or at least much better than non-transit-accessible real estate's rate).
Taxing land also discourages hoarding of parcels as empty parking lots (and discourages surface parking, generally).
Meanwhile, you are picturing a conventional Property Tax on the whole value of property. You are correct that Property Taxes discourage improvements like TOD and actively encourages disinvestment (knockingn buildings down) and the games that Don Chiofaro is playing with his Aquarium parking garage--he can afford to keep it as a garage (a transit-accessible garage!) because as a crappy old thing its taxes are low even as it throws off abundant cash. Tax the Land (call it the Aquarium TOD TIF district) and shift the burden to the land but dangle low taxes on a tower and suddenly he's motivated to tear down the garage and build a tower to ease the bite of the tax on his land.
Left with surface parking or just scruffy single-level stuff, owners realize that the Land Value Tax is proportionately too high a % of what they have invested. Their solution is to average down by shifting new-construction/renovation dollars to the parcel, the more the better since it it tax-advantaged and averages them down further. (or to sell to a developer)
There is also a SERIOUS flaw in the Seaport where we basically got all the "TOD" but the McCourt family pocketed ~$200m dollars *for just holding 25 acres of land* (not being the eventual developer) That value was created by our transport spending (Silver and Big Dig), not by any work the McCourts ever did (in fact, they held it as surface parking for perhaps longer than they should have, as they were waiting for a bigger future payoff...a split rate tax discourages this kind of land hoarding and encourages immediate & larger improvement)
Worse, the Seaport will strangle on its traffic and lose its TOD bias because we don't have the money to upgrade the Silver Line (larger fleet, T-under-D), and all the Land-Value upside created State investment has disappeared into either private hands or into the Boston City general fund (where it loses its "pay it forward" dynamic)