Your vacuum tube transport system reminds me a lot of the Pneumatic Diversity Vents from Portal 2.
Those are tubs that carry various items, like cubes or turrets, throughout the massive Aperture Science Laboratories.
In the cooperative campaign, Atlas and P-body are moved from chamber to chamber or from/to the hub using those tubs; and the level "Tube Ride" in Chapter 5 in the Singleplayer campaign, features a tube ride from Chell's point of view.
GLaDOS can control if any section of this tubes is active or not, and, in some cases like in "GLaDOS' Lair" in Chapter 5 in the Singleplayer campaign, GLaDOS is able to move tubes arround.
Those Pneumatic Diversity Vents have "Passive Monitoring" that controls which items are in the tube, and allow to bifurcate them in different directions.
So GLaDOS, or anybody else that has control over this massive tube network, can activate a tube route to move items (or persons) from one place to another as always as there is tube coverage.
OK, now out of this Portal 2 system; in the reality this would be a really expensive system, just constructing these tubs will be a massive cost, and keeping them running will have an enormous electricity cost.
Also, we will need to take care of leaks and have some system of "emergency exits" to recover items that might end up trapped in a tube region where it is not working properly and it cannot move the items.
Replacing the current package mail system for this vacuum tubes will require massive modifications into the structure of the buildings in order for these tubes to fit properly. The best way to make them fit will be to create new buildings with a structural design compatible with those tubes.