The value of the color marked as transparent is not discarded, but blended with background using "add" operation if the background isn't transparent.
For example, here is an image that is transparent, but the color of the transparent index in it's palette is set to #804000:

var assert = require('assert')
var Canvas = require('canvas')
var c = new Canvas(150, 150)
var ctx = c.getContext('2d')
// fill background with something non-transparent
ctx.fillStyle = 'rgb(0, 100, 200)'
ctx.fillRect(0, 0, 150, 150)
// load the (supposedly) transparent gif
var i = new Canvas.Image()
i.src = 'transparent.gif' // https://i.imgur.com/XCz0eVi.gif
// draw it on top of our background
ctx.drawImage(i, 0, 0)
// expect no visible change in the canvas
var pixel = ctx.getImageData(0, 0, 1, 1).data
assert.deepEqual(pixel, [0, 100, 200, 255])
The value of the color marked as transparent is not discarded, but blended with background using "add" operation if the background isn't transparent.
For example, here is an image that is transparent, but the color of the transparent index in it's palette is set to

#804000: