That was my impression as well. The bonus ones were literally just that, a bonus for causing a bit of carnage in an area. The alternative was to write another poor quest with a thinnly veiled goal of causing carnage in that area of the map, so at the end they were just a precursor to world quests in a sense. Apexis were hated because they were used instead of actual progression systems in story relevant parts of the game, as well as being pretty much the only ones, hence they were hated (i did too).