By default, I wear my gaiters under my waterproof trousers, as I’ll start off with them on over top of boots and trousers, and invariably pull on waterproofs after when it starts to rain. This means the water runs off and over gaiters, so works well.
Not having gaiters, and wearing fabric type boots, I have had days where the wet grass has caused the outers of my boots to get soaked, and ‘leak’ over and into the inside. Gaiter help this no end.
As for the pack rain covers, I reckon the rain runs down the straps and inside the rain cover, so I never use them. I have all my kit in dry bags, not only does it keep stuff dry, it means I know where everything is, which works really well camping too.