The elephant in the room is the way sometimes whole companies need to migrate away from a highly optimized workflow in order to conform to some non-custom software, specifically because the workflow is not extremely generic. It doesn't take too many of these packages before optimization and efficiency are beyond the horizon and no longer in the rear-view mirror. The electronic equivalent of one paper cut at a time for everyone who touches it.

This can lead to ingrained violations of Conway's Law up and down the line.

It can be more difficult to see the forest for the trees when the elephant has grown bigger than the room.