I guess that's a fair counter-argument. If more GPUs start using X8 or even X4 (gosh!), then having a PCIe5 X16 slot will indeed be better over the PCIe5 M.2 ones (assuming lower end GPUs are indeed PCIe5). Do I want that to happen? Hell no. Unfortunately, it seems like that's a very plausible future for the lower end though, so it can't be dismissed.
For the higher end of the spectrum (GPUs, that is), it's a non-issue though. PCIe4 vs PCIe5 for a full X16 slot, I'll venture a guess and say it's a marginal difference and, more than likely, imperceptible. So a lower end board with a higher end GPU should be a non issue for a PCIe4 X16 slot.
Regards.