Seems some of the CPU board designers didn't think about the thermal issues. When the CPU is put on the side that is agains the motherboard the heat has a hard time to escape.
It also confused me slightly 
Btw, how many layers is the A4000 motherboard?
You mean Commodore A3630 CPU board. It has CPU and all components on bottom side because that side was paste soldered and the other side was wave soldered. On the top side small raster SMD componts or any components including plastic would have short circuited by tin or melted by tin. It has always been possible to add SMD componets to wave solder side too, but they have to be glued or otherwise they are sucked by wave and sank to a pool of tin.
I think Commodore designers had no choise since company policy was always to reduce costs. Think about A4000cr Rev D where cr means costs reduced. It is always a bad idea to name products with terms indicating costs which will give negative impression about quality.
The other ways to do A3630 would have been
1) to put 680EC030 to top side and paste solder 2 both sides of PCB and then hand solder connector and all through hole components like for example jumper headers. This would have been very very slow and very expensive in production.
2) to put 680EC030 and every component to top side then paste solder it and then hand solder the connector to the other side. This would have been very slow and expensive in production too.
There are 4 layers in A4000 PCBs. Which you might already know.
And yes also 680EC030 would benefit of cooling, since my experience has taught that it is possible to scorch 680EC030 with heat. I accidentally misjumpered/overclocked A4000cr Rev D and 680EC030 got broken with motherboard always showing yellow on boot. I then desoldered broken 680EC030 and resoldered 68030 desoldered from a piece of sawed Apple motherboard. Quite a job to do it, but I think now this could be the only A4000 motherboard in the world with real (non EC) 68030 on motherboard and why not since 680EC030 was just another cost reducing thing.