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The chipset just multiplexes and it's fine. You're unlikely to actually use more than 16 lanes simultaneously in such a setup. But yes, Intel is being overly stingy with PCI-E lanes off of the CPU and leaning heavily on the chipset to compensate. I'm hoping Ryzen 3rd gen bumps the lane count a bit more, otherwise Threadripper's 64 lanes look mighty nice...
The new Ryzens are meant to launch with PCIe 4.0 (this summer, I'm due an upgrade!), so effectively... I'm surprised they don't come with more, especially many of the current ones come with 2-3 x16 slots, AND 2-3 M2s.. Both Intel and AMD have been adding more cores recently. Plus, if you're doing any GPU-based rendering, they're going to simultaneously move data back and forth from NVMe to the GPU's memory. But it gr…
Games definitely don't do this at all, which is the primary market for a discreet GPU in these consumer platforms.
When they do stream in assets they do so slowly & in a controlled, rationed amount to minimize impact on FPS. They are far from being PCI-E bandwidth limited. That's kind of why you see almost no FPS drop at all when restricting GPUs to x8 bandwidth, even.
If you're doing something more workstation-y or custom, that'd be when AMD & Intel would point you at the HEDT platforms which have more than 16-20 lanes.