I see PCIe-4 (and 5) being a boon to APUs for several reasons:
1) The link to the I/O chip gains a lot of bandwidth for situations where those are used.
2) NVME drives can run on 2 lanes instead of 4 for the same performance, giving the possibility of either running extra NVME drives, or reducing the cost of implementing them
3) The 8 PCIe lanes that the APUs currently expose to the motherboard slots will be able to be effective for higher end GPUs (that are configured for PCIe4 and 5) without diminishing their performance.
4) With lane bifurcation, the APU can directly run a 4x PCIe 4 slot for a mainstream card and still have 4 more lanes for additional slots.
5) Cheaper NVME drives can operate with better performance by using HMB instead of on IC DRAM for scratch memory. The faster NVME/PCI connection means more available bandiwidth to the host to access the DRAM, and with the expected capacity increases coming with DDR-5, the host will have sufficient RAM for the buffering to not make a significant impact on system performance. The higher DDR speeds will also enhance this functionality.
6) With a potential chipset driven Thunderbolt implementation in the future, having the higher PCIe bandwidth between the CPU and the chipset will allow that to perform more closely to its expected levels.
All in all, I think that APUs will definitely enjoy a lot of benefits from PCIe 4 and 5, though those won't all be evident in every implementation.