Even more than the PCI-lanes, there wasn't hardware to justify it. With Apple Silicon, the GPU is built in and you can't fill the case with cards from NVidia to make it a CUDA-monster or handle graphics beyond the (impressive) abilities of the combined CPU/GPU.
Exactly this. Apple neutered the Mac Pro by making all of its additional functionality useless.
Years ago, they announced that they were killing support for kernel-space drivers. Then they announced a user-space replacement, DriverKit, that is basically half-assed when it comes to PCI, providing no support for any of the sorts of PCIe drivers that anyone would actually want to write. The operating system already comes with built-in support for USB xHCI silicon and most major networking chipsets, nobody builds PCIe audio anymore, FireWire support is dropped in the current OS release, and video drivers can't be written because Apple didn't bother writing the hooks.
That last one is the showstopper for PCI slots on a Mac. The main reason people bought Mac Pro or bought Thunderbolt enclosures was to support high-end video cards. With Apple not supporting any non-Apple GPUs on Apple Silicon, the slots are basically useless. I'm not saying that PCIe is useless by any means, just that the neutered, broken, driverless PCIe-lite hack that Apple actually makes available on macOS is basically useless.
I suppose you could theoretically provide DriverKit support for RAID cards, but really at this point everybody just uses external RAID hardware attached over a network anyway, so the number of people who would buy a Mac Pro for something like that is negligible.
And I guess in theory, you could port Linux video card drivers over if the only thing you're doing is using GPUs for non-video purposes (e.g. for AI model training or offline 3D rendering), but tying it into the operating system as a video output device is likely impossible without additional support from Apple, and nobody is going to bother to do that for the tiny number of people who would want that when you can just run Linux on x86 and not have to do all that porting work. After all, for those sorts of tasks, you probably aren't benefitting much from the OS or the CPU or memory performance anyway.
So basically the Mac Pro was dead on arrival because of Apple dropping support for very nearly every single thing that the Mac Pro could do that couldn't be done just as easily with a Studio (without even attaching a Thunderbolt PCIe enclosure). And once the Studio came out and had a comparable CPU in a much smaller form factor, the writing was on the wall.
More than that, the Apple Silicon Mac Pro is a sad toy that was never truly worthy of the Mac Pro name by any stretch of the imagination. It doesn't even have ECC memory or upgradable RAM. IMO, Apple really should have just been honest with its pro users and said "We no longer care about you," and then they should have dropped the Mac Pro as part of the Apple Silicon transition, rather than shipping something so massively downgraded that is so many miles from being a true pro desktop machine.
Anyone who is even slightly surprised by it being discontinued was obviously not paying attention.