To reproduce:

1. Open the project, attached by user
2. Build & Run for WebGL
3. Observe the size of the canvas

Expected: specifying width and height parameters in UnityLoader.instantiate should resize the canvas by the specified values
Actual: specifying width and height parameters in UnityLoader.instantiate does not resize the canvas by the specified values

Reproduced in 5.6.0f1, 5.6.0f2, 5.6.0f3, 5.6.0p1, 2017.1.0b1
Could not reproduce in 5.5 or lower, because this feature does not exist

By design: you need to specify whether width and height are pixel, percent values, etc.. for example:
var gameInstance = UnityLoader.instantiate("gameContainer", "Build/test.json", {width: "200px", height: "200px"});
or
var gameInstance = UnityLoader.instantiate("gameContainer", "Build/test.json", {width: "50%", height: "50%"});