Well, usually the point of upscaling art is to arrive at a more detailed image that is clearer and more readable so that it represents a higher pixel-resolution that has less abstraction you'd get with a lower-res.
What you're doing here is no different than painting with broad brush strokes and then reducing the brush size and going back over it with consecutive passes. The only difference with that is you are confining the larger brush to a square grid. But then you try to remove that in your consecutive passes.
My understanding is pixel art shines because of the ways a limited pixel grid compels the artist to find all kinds of creative solutions in terms of emphasizing clarity, priority of detail, inferred detail etc. That gets diminished when artists go for finer detail grids so I feel it's a different thing to what's being proposed here. Visible jaggies on their part are a natural consequence that comes with limited pixel grids, but are they a goal in and of itself? Maybe they distract from the true qualities (whatever those might be) of pixel art even?
An upscale filter is an automated process, so while it preserves the original grid it undermines the whole point of being in control. But a manual second pass... that's a different story.
Interesting stuff, I'll try it out.