Because they usually have to use a different more expensive chipset and a lot of stuff uses PCIE these days that didnt before, for example NVME SSDs now take PCIE slots that were free to be used for different stuff before. And in the desktop market, most people just dont need more than a pcie slot for their boot drive and their GPU. Add to that that PCIE 4 and 5 are more expensive and require more expensive boards.