It's a problem with drawZoomedText. Using drawText will render correctly with the semi-transparent pixels, but drawZoomedText with zoom set to 2 or 1 will not draw them.

https://rpgmaker.net/users/Beaker/locker/main.rfn
// main.js automatically generated by Sphere Studio
// Vanilla compiler plugin
font1 = LoadFont("main.rfn");
font2 = LoadFont("main.rfn");
var c = CreateColor(255,0,128,255)
font2.setColorMask(c);
function game()
{
var txt = "SeT GQwWoO!";
while (true)
{
font1.drawZoomedText(0,0,2,txt);//renders without alpha
font2.drawZoomedText(0,20,2,txt);// ..
font1.drawZoomedText(0,40,1,txt);//also renders without alpha
font2.drawZoomedText(0,60,1, txt);// ...
font1.drawText(0,80,txt);//Render correctly
font2.drawText(0,100, txt);// ..
FlipScreen();
}
}