These first Apple Silicon Macs are to replace the lowest-end models of the Mac, but all the higher-end computers are coming in the next year or two. The 13” MacBook Pro has been two confusingly-similar computers for 4 years: the entry model is basically a thicker MacBook Air for people who want a Pro (in 2016, this was the MacBook Pro without a Touch Bar with two USB-C ports), they now have the Touch Bar but still 2 ports.
When you go to buy MacBook Air, all models have been replaced with M1—because the M1 models are faster & better in every way than the previous generation. Whereas when you buy the Mac mini & MacBook Pro, they’re still selling the higher-end models powered by Intel, including the 4-port models, because the first wave of Apple Silicon doesn’t replace those models. The inclusion of 2 USB-4 ports is because the M1 chip itself includes 2 USB-4 bridges built in, & by using the same chip across all the computers, since the MacBook Air only has the two ports, they had to standardize the design. (The Mac mini also has USB-A ports, which I assume are powered by some separate PCIe components outside M1.)
Next spring, I would expect a new M-series chip (M1X?) that will power the Pro models of the 13”, the 16”, the iMacs, etc. (My guess is the 21” iMac will be the first to be physically redesigned; it is so old at this point.) It will most likely include 4 USB-4 components, & all of those models will have the 4 ports. Apple is not giving up on 4-port models, they just wanted to start at the low end & work upwards with the transition. I think this was made clear by the continued selling of Intel 4-port models—whereas if they thought the Apple Silicon model would fully replace that I think it’d be gone, since they want to move as many people to Apple Silicon as quickly as possible. (Apple will keep the Intel Macs around for a period, since various enterprise/education customers want them, but.)