You can still get mainboards for modern CPUs (e.g. Intel Skylake) with PCI slots. Not sure how they work internally, e.g. if there is a PCIe bridge and if yes on what level PCI emulation happens.
PCI is a CPU-independent bus (unlike AT/ISA), it isn't really emulated, rather, there's a host bridge on these mainboards that connect it to PCIe from the CPU or southbridge.