How about a video? This is an example of rendering artefacts that get introduced when boosting the resolution. Gran Turismo 2 is also one of the least problematic games but the side mirrors rendering issue is well known. It's also one of those things than you can never un-see so apologies to anybody still playing GT2 via emulation.
Rather than post evidence, can you please include the argument. You wouldn't at a trial just drop Exhibit A on the desk and expect everyone to infer the meaningfulness of it.
Watching that video, I see a number of points that confirm to me higher internal rendering:
1) The boot scene, the Sony and PS logos are very clean where the text is pixelated. If de-pixelising of the output buffer is in effect, that should affect the text as well as the logo.
2) There are clear differences between clean geometry and pixelated textures. Here we see clean lines around the model silhouette, and chunky pixels from the texture.
I'm not seeing anything around the geometry that's an artefact or fault or not what you'd expect from rendering natively at that resolution. This extends to all signs, fences, and buildings. Evidence is the emulator is rendering to a 1080p framebuffer, drawing the geometry at that resolution.
Edit: Same sampling Duckstation for Wipeout. In this vid, 2D upscaling is being applied to the interface while 3D rendering is native, no obvious artefacts that I can see.
And this one of another example you cited, Tomb Raider. We see the pixelated rendering of the low video, the pixelated loading screen, and then clean, crisp geometry the moment we start rendering the game properly:
What's more interesting is we can see the 2D upscaling in effect on the textures, producing the classic 'blobbiness' of 2D upscaling that is completely absent from the geometry.