The clashing pixel scales bothers me way, way more than the text being offset by one pixel. Looks really nasty. But I doubt the offsetting would matter to me too much, even in motion (more than the pixelation in general, anyway.)
The ideal of pixel art is that each pixel is carefully and deliberately placed for maximum effect. When you use "enlarged pixels" in one area of an image you're stating at the best way to represent something is as a series of squares, but it usually isn't.
This is a problem I have with pixelated graphics in general but unfortunately not everyone can afford to go for high-res 2D/implement decent TV shaders as an option. Of course ideally I'd be playing all of these games (and emulating) on a good CRT with the programs outputting at native res but I can't do that right now and I don't think Game Maker or other software even supports that, etc.
If you really want to go for the NN pixelly style then prescaling art can probably have some benefits for certain scenarios, e.g. imagine a game where everything normally moves aligned to the grid but then you can activate bullet time and everything halves its movement speed (so it looks smoother.)