When a skin is the wrong tool

If you find yourself replacing structure rather than appearance -- moving regions, adding a block the engine does not build, needing markup that does not exist -- a stylesheet has stopped being the cheap option. At that point editing the template is more honest, and you should know the price you have just agreed to: every engine update can conflict there, and docs/decisions.md explains what the templates promise and what they do not.

The other honest answer is that the engine may simply be missing a setting. If a skin has to fight a region into hiding, say so -- a switch for a region is a reasonable thing to ask for, and cheaper for everyone than the CSS that fights it.