Seems that U-boot 202407 (not 202407-rc5) has already pushed PCIe 3.0 for Mediatek MT7988 driver in mainline. But still missing DTS patch for PCIe.
I was able to build 202407 with partial patch from original patch, just to add missing devices in DTS and is working.
Yes,dts patches are rejected because boards are not of_upstream yet,but good to know that dts patches still working…christian made a bit different handling of the optional phy…only tested it with of_upstream conversion