Not sure about Pixi and Animate CC, it likely has to do with the setup and how both work with each other. Never crossed my mind to use the two together but I'll be looking into it.
You could simulate that effect within Animate CC without having to use Pixi. It's not (currently) possible to natively animate the native filter effects in Animate CC since they've disabled that for performance reasons (see this link, Filter and Color Effects section). However, like that doc recommends, if you make a separate clip with the filter applied to the object, you can tween that clip overtop of the other clip (fading the blurred clip in and out), to simulate a blur effect.
Sounds like the animated mask was a separate issue (it is possible, and easy, to do that with Animate CC using the timeline -- just make a keyframed mask layer with no tweening). As far as creating an animated mask via hand-coding with DOM elements, I guess you could use SVG for the mask and create a sequence of masked clips that you turn on and off. Otherwise, I don't think it's technically possible to do animated masks with actual DOM elements unless you're just using rectangles and square masks, you're back at using canvas at that point, and might be a fairly complex task to do if you're not familiar with it.
it'd be cool to see some sort of library / plugin to make doing this specific task with canvas easy (cough cough).
Agree that you should learn to hand-code too and make that part of your arsenal but don't throw away your timeline skills! There's a reason why apps like After Effects exists