SC3K’s art was not “crafted pixel by pixel.” It was rendered from 3DS Max. Maxis released a version of G-Max called the Building Architect Tool that included a template with the same lighting rig that they used for the in-game assets. This tool rendered and exported the various zoom levels and orientations.
You're describing SimCity 4, not SimCity 3000. The SC3k tool is not entirely 2D, but it does mostly behave like one (with emulated voxels instead of pixels).
And while I cannot confirm what Maxis was doing internally, I am quite sure no-one was using 3DS Max for rendering game assets in the 90s considering it had just been released and well into the 2000s it was still humongously slow.
The art looks very rendered, with pixel cleanup in something like photoshop. I was using 3ds Max on my norma PC circa 2001-2002. Game studios should definitely have had 3d studio in the mid to late 90s on their actual workstations if they were Windows based (or lightwave). Crucially, The Sims (3ds max) released quite close in time and we know 4k was also 3dsmax, so I think it’s fairly safe to say Maxis was a 3ds shop in this era. It was ubiquitous in pc gaming of the era.
In the 2000s SC4 was already using 3DS Max, but here we are talking about a game that started development in 97. And they already had 3D games before it...
In SC3k sprites you can also clearly see two different grid sizes, so at the very least the retouching and some props are "pixel art".
quite sure = confidently wrong
Though they are absolutely right that I confused SC4’s BAT with SC3K’s.