It can be a space saving and packaging solution, it can be a historical leftover, or many other reasons.
Not optimal from a heat management POV but not the end of the world, either.
Example of the Mk4 Golf/Beetle - 1.8 was counter flow and the 2.0 was cross flow, both used the same HG, difference was in the rods and pistons.
Anyhow, the common upgrade was to put the 1.8 head on the 2.0 block, instantly get more CFM.
Even after careful working of both heads (full on, proper, CNC stuff) the 2.0 head could only match the 1.8 head, never exceed it.
So flow is not always compromised in the counter flow style head.