You're right in that there's nothing stopping one from doing so (I even use an integer scaler for old games on my main computer), it's just a tradeoff between "doing what's possible" and "having the
most authentic experience one can".
If we're talking about the subjective experience of recreating "a child's bedroom computer" from the mid 90s-early 00s, a widescreen aspect ratio alone would be jarring, since my conception of a monitor for such a system is a 4:3 CRT. So for me, little else would reach that level except a system with the same aspect ratio and a similar DPI.
Not only that, but UI design itself has undergone many shifts since that era to account for the types of monitors those UIs are being designed for. There's not as much of a need for pixel-perfect design when vector-based web UIs dominate the desktop application space nowadays, relegating those that go back to older UI paradigms to enthusiasts who still remember earlier times. Or maybe people who develop for fantasy consoles.
I should mention while I'm at it that those sort of faux-pixel art shaders used in some games come off as quite jarring to me since I expect UIs to be meticulously laid out for the original screen size, not just for blowing up arbitrary content 2x or 4x on a huge widescreen monitor. I sometimes feel those are meant to represent a nostalgic feeling of some kind, being pixelated and all, but really it just makes me wish there were some alternate reality in which people still designed games and desktop applications for 800x600 or 1024x768 monitors again.
It's interesting at present how there's stuff like 4K and then there's the playdate with a relatively tiny handheld resolution, but relatively little interest for new content for those types of resolutions in-between.