Btw, the boxes you drew don't match the layout pic you provided. You show two slots above the PCIe x16 slot and one beneath it, while the layout image shows one above and two beneath. Looking at the images you provided, I'm pretty sure the layout image has it right. The GPU itself is very very thin, it's the fan assembly that takes so much space, and it's all on one side of the card. That would hide a PCIe x1 slot very easily, whereas you'd see two slots above the GPU clear as day.
Intel Xeon w7-3465X OC | Asus Pro WS W790-E Sage SE | NVIDIA GeForce RTX 4090 FE | 8x16GiB G-Skill Zeta R5 DDR5-6000 | Windows 11 23H2 | (details)
MacBook Pro 14in | M1 Max (32 GPU Cores) | 64GB LPDDR5 6400 | macOS 13