Overall, very nice piece of design job However, I (personally) still have some doubts about a choice of 40mm fan. Please let me explain.
First of all, I would like to say that I have zero interest on what the final board will look like, it is certainly yours and only yours decision. I am not planning to manufacture and sell any new rev. boards either, certainly not in forseeable future. My involvement ends as soon as I deplete current components inventory and that only goes for my current stock of 2.7 PCBs.
Now back to 40mm fan choice: Looking at previous renders of some 4.x or perhaps 5.x PCBs you posted earlier, it seems to me that the PCB will partially block active fan area to some extent (the air flow cutout is not in full circle). Without an access to the source data I can only estimate that about 30-40% of effective airflow area would be blocked like that.
I also assume, that due to requirement for future expansion, maximal height of fan is limited toperhaps 13 mm.
Therfore, I am gonna compare two 5V DC fans that fall into such cathegory and I would probably have chose for the design and build:
40x40x10mm; 11,9m3/h; 27dBA; slide bearing, about 3 EUR/pc
25x25x10mm; 5,1m3/h; 16dBA; Vapo technology, about 6 EUR/pc
Please note that Sunon does not have ball bearing fan in 40x40x10 mm, which really is mass product cathegory, while 25x25mm fan are provided with Vapo technology. Vapo is recognised as superior to former one and of course we all know weaknes of slide bearings. That on the other hand explains the price difference that I believe is well justified in this case.
Anyway, knowing you block lets say 35% of effective airflow with PCB, 40x40 fan would only push about 7,2m3 of air per hour. On the other hand, 25x25 fan would push 5,1 m3 of air per hour. The difference is some 30 percent.
Most importantly is what that PCB block to the airflow on 40x40 solution would do to noice and fan lifespan. Of course I have not done any calculations or measurements, but I can guarantie they both will be impacted severly. In result, 40x40 fan will certainly not have 27 dBA noice level as per spec, it will be far worse. And 27dBA fan is one of the lowest value fan I could pick in that cathegory.
Mechanical aspect of that airflow blockage will be that the air whirls will cause fan to vibrate, severly decreasing fan lifespan and slowly killing all the onboard connections and causing stress to all (especally) BGA components.
Frankly speaking, I do not even think, that having any kind of fan screwed up directly to the PCB is a good idea at all. Certainly not without some silicone vibration dampers.