GPU cards in PCIEX16_1 and PCIEX16_3 will run x16/x16. But populating PCIEX8_2 or PCIEX8_4 runs these GPUs at x16/x8.
And populating PCIEX8_4 disables motherboard M.2 lanes (even with 40-lane CPU).
This seems to be a "hardwired" design configuration, firmware (BIOS) apparently cannot reconfigure it.
People have requested/demanded this firmware function before, on two X99 R5E motherboard versions, and it never happened.
(I was always disappointed that X99 x16/x16/x8 was not an option, let alone Intel's promised X99 x8/x8/x8/x8/x8, haha.)

The 512GB 950 Pro has rated speeds up to 2500MB/s Read, up to 1500MB/s Write.
4xPCIe3 can support up to 3940MB/s. 4xPCIe2 can support up to 2000MB/s. 4 lanes used in CPU PCIe controller either way.
(You might be observing ~1500MB/s because your PCH-to-CPU DMI2 bandwidth is saturated by M.2, SATA, USB, network, audio, and other devices.)

As you've observed, you can't have it all simultaneously and your best options for installing both GPUs and both M.2 SSDs on this motherboard are:
- GPU cards in PCIEX16_1 and PCIEX16_3 (SLI x16/x16) and 950 Pro adapter in PCIEX4_1 (running up to 2000MB/s), or
- GPU cards in PCIEX16_1 and PCIEX16_3 (SLi x16/x8) and 950 Pro adapter in PCIEX8_2 (running up to 2500MB/s).

Yes, it's because of the motherboard design. But none of the other X99 motherboards is any better, they each have their own performance tradeoffs (except perhaps the X99-E WS, with its PLX/PEX chip).

So which performance metric is more important to you?

Does x16/x8 actually reduce your raw fps?
Probably not. At least not very much and only rarely, especially since first GPU gets most of the unbalanced workload.
(For perspective, run your games and your benchmark engines. Actual fps matters, synthetic scores don't. Some games balance multi-GPU loads better than others and might actually see a few more fps at x16/x16 under peak loads, but most games handle multi-GPU poorly and would see no difference at x16/x8.)

Does 2000MB/s actually slow down your loading times?
Probably a little. But not much and not often, since most system access is on the faster and bigger M.2 SSD.
(For perspective, a 100MB sequential Read at this speed takes 0.05 seconds instead of 0.04 seconds. How often do you do huge sustained multi-GB Reads off your secondary SSD which would be slowed down by more than an imperceptible fraction of a second? And can your system actually use >2000MB/s of non-system data without processing slowdown anyhow?)