As someone else already pointed out, the M4 Pro Mac mini gets copper cooling, whereas the M4 Mac mini gets aluminum. This is similar to the Mac Studio where the Mx Ultra gets copper cooling, but the Mx Max gets aluminum.
It would appear Apple believes the same form factors of the Mac mini and Mac Studio can both accommodate two different classes of chips in terms of power consumption and heat dissipation, but require different cooling methods to accomplish this.
The good news that outside the quiet whine with the M1 series Mac Studio, very few people complain about noise with the Mac Studio even under moderate to relatively heavy load, whether it's Mx Max or Mx Ultra. I would hazard to guess that Apple has engineered the Mac mini with somewhat similar noise level targets, for both M4 and M4 Pro.
In contrast, the 2017 iMac Core i7 I bought was as loud as a vacuum cleaner after 30 s of full load. It was a disaster. I returned it and bought the mid-tier i5 (not even the fastest i5) and it was silent. It was awesome in comparison. Interestingly, the iMac Pro, released the same year and in the same form factor, was silent under similar loads despite running much hotter CPUs. Apple redesigned the cooling to accomplish this. Too bad they didn't use this cooling in the i7 model.
Yes, I was overjoyed to see 5 ports on the M4 Mac mini. I was hopeful for that, but was not expecting it all, especially since there are only Thunderbolt 4 controllers in M4 and because Gurman said there existed a 3-port version in the labs.
I was fully expecting the M4 Pro to get 5 USB ports, but yes it's a downer that it's fewer than before. OTOH, those three Thunderbolt ports are Thunderbolt 5. Maybe they will better support high bandwidth Thunderbolt hubs... well maybe 2 years down the line when they actually exist.
The US$400 price premium for the M4 Pro in the Mac mini is irritating though. It's only $200 in the MacBook Pro. If the M4 Pro had been only $200 more, I probably would have bought it, even though I don't need it. You lost an upsale here Apple!