If you want to connect multiple sources togther, how they are created is very important.
It certainly can be a consideration, but still does not dictate what we choose to use as a reference. We can still wire our circuit using two voltages with opposing phase angles rather that two voltages with the same phase angle.
If you have a 120/240 volt source, what person in their right might would seek to add another transformer and bring in a different 120 volt source because they need a second 120 volt sources in phase opposition? It is not a math trick, it is a physical wiring connection that gives you two voltages that are not in phase.
What is confusing the whole deal seems to be the concept of reversing polarity. A phase just a single alternating emf across two wires. Chosing a polarity for one voltage does not dictate the polarity of the others. Some transformer connections even make use of the fact that you can use them in a polarity that is different from the others in the bank. What you wind up with is a physical difference in the output voltage, not a mere "math trick".
Truly if you swap the two wire ends, you have swapped the polarity and it is just the negative of the other. There is nothing that says there is a universal constant for determining which of the two wires should be the reference end.
The addition of the center-tap now gives us two different pairings. Now we have two voltages that are equal in magnitude. We can now supply two different circuits with two different emfs. We can choose to connect these so they can either have the same phase angle or not. It is a physical connection and is how the system is defined. The polarity of one voltage does not dictate the polarity of the other.
You will get the same voltages even if you use two completely different primary sources. Nothing in how these two voltages are created is going to ultimately determine how we use these two separate phases as far as the polarity is concerned.
The reason we call 120/240 single-phase is because that is how it is used. We have single-phase 240 volt loads, and single-phase 120 volt loads (two different sets of loads: one set for each side of the winding).
There is nothing that says we can't use the two 120 volt sources together in phase opposition to supply two phases to a two-phase load.