Old games mostly did use the actual color palette of the computer(fullscreen only games were fullscreen for that reason I think), by changing it, and so they just did "do not render color #0" for exemple, that applied everywhere.
Now the Webgl effect does not work like that, it ll check every pixel of the image, and change some of them, which can be intensive.
At the end transparent is an information, like magenta was, the only difference being that, since nothing renders it, it appears transparent in every image editor (however it is line the magenta, still an information existing, and so will be stored in memory)