Its not just leaving a mark. You actually claim it for the inquisition. That means when you claim Redcliffe, you actually occupy a town in Ferelden, and call it your own.
The landmark journal text says "Any navigator worth following will look out for distinctive landmarks that provide bearings and define regions.", which can be interpreted as a peaceful action.
As to locations being "under the protection of the Inquisition", the Inquisition forces are the only ones actually doing something to protect people and to fend off the demons - as many NPCs tell you. Which is presumably the main reason the Inquisition gets the constant influx of recruits.
Where are the Fereldan forces anyway? The only ones I recall seeing were with Anora/Alistair. And the Orlesian forces are apparently at the Exalted Plains busy fighting each other. Or they would be if they weren't so afraid of the corpses to actually leave their forts. "Come here, you foul corpse, and I shall taunt you a second time!"
And what about the Venatori - a bona fide hostile foreign power. They get to establish camps and strongholds and deploy troops pretty much all over the map. I am more surprised that no Fereldan/Orlesian action is being taken against them.