1x1 pixels for padding and aligning were absolutely a thing in the late 90s (1997+). Don't know what alternative history you have in mind, but it was used at the "table layout" era.

What came later was the float layout hell- sorry, "solution".

The 1x1 pixel gif hack arrived shortly after Netscape 1.1 introduced tables. I belive this was before colored text and tiled backgrounds became available. So the hack is definitely part of the “golden age” of web design.