Phasing is more than the building wiring. You are correct that transformers should be plugged into the same side of the house wiring,
Even apart from the house connection, the transformers themselves have to be in phase. For example, take 2 simple transformers. The manufacturer may have wired either end of the polarized line from the 120-volt outlet to either end of the primary, or may have taken the terminal feeds off either end of the secondary. Thus, you can't always relay on a polarized plug. There are transformers in use today which differ within the same model number. Lionel and MTH have both experienced this.
Thus, one should always check phasing when there are multiple transformers on the same layout, even if one is not used for powering trains, because there is always the chance of a cross-connection. If you have 2 transformers, each at 18 volts, and the phasing is crossed, a roller pair across the gaps causes a 36-votl short. On most transformers, not all terminal posts are fed through a breaker. For example, many post combinations on a Lionel Type R are unbreakered, as would be a short among the A,B,C,D terminals of a pw ZW.
FYI, a short or high currentthrough pickup rollers can ruin the springs in them, and I have had axles get very hot without blowing a breaker, as amperage was within transformer breaker limits.
Something has to be wrong, because if the boards overheated, the current had to be flowing through them, and this normally doesn't happen in a short on the tracks. This is why I use external breakers with low ratings. Note also that a TVS does not limit current flow; it bleeds off excessive voltage.
I can't see how coupler coils would have burned out, unless the wires to them made contact with something. Check the locos and see if the wires from the pickup rollers could possibly be touch the wires that feed the couplers. On several of my locos, they come through the same hole, and could be subject to insulation chafing.
This situation bears careful analysis before settling on TVS as the preventative.
