It is important to distinguish between physical lines (the branches of the infrastructure) and lines of route (the paths services follow over the network). The colours on the Metrolink map represent routes, not physical lines. For example, Altrincham - Bury (green), Altrincham - Piccadilly/Etihad (purple) and Bury - Piccadilly (yellow) are different lines of route that run on the Altrincham and Bury physical lines.
In using colours to help distinguish between routes on the map, TfGM has followed common practice on maps of rapid transit systems worldwide. But those other system maps usually have a key that translates the colours to route numbers, letters or names, or have "bubbles" with the route identifier at each end of the route. Journey planners, scraping the data off the map, can then describe the line of route as "S2" or "Metropolitan" or whatever. The Metrolink map, however, just has the colours as the only means of identifying the routes. Therefore it is logical for Google Maps and other planners to describe the line of route as "Green line" or "Purple line" etc. The algorithms are not to know that TfGM has chosen not to refer to the colours on the tram destination displays and PIDs.
If the colours "just aren't a thing", TfGM should take them off its map. When you publish data, you must expect it to be used.