The rooms that Capcom DID re-render in 3D have not been modified. I should note that the pack is not entirely complete so not all the textures have been upscaled. More detailed comparisons along with info about the project can be found here This release currently contains more than 1600 replaced textures between gameplay and cutscenes. At its best it matches the RE0 Remaster in terms of quality.
Luckily a modder by the name of Shiryu took it upon themselves to re-upscale the backgrounds by running the original GameCube ones through Gigapixel and ESRGAN. Some looked incredibly compressed and blurry, (especially the pool draining one) as they were originally meant to be shown in a 4:3 aspect ratio and at a much lower resolution. While the game is at LEAST 1080p, the same could not be said for the handful of pre-rendered FMV cutscenes which play during scripted events. It was clear that Capcom didn't re-render new backgrounds like they did with the RE0 remaster, and instead cheaply fed them through an upscaler with a wax filter. When the HD remaster released back in 2015 there was some fussing about the remaster's visuals compared to the GameCube original.
