Hi, yes they do, you can choose which scenes are affected when you create your filter.
Viewing post in [CGMZ] Pixi Filters for RPG Maker MZ comments
Hi, if you are looking at the plugin parameters, those are just preset settings (for example, if you want the same Godray to appear across multiple towns in your game, you can create a preset in the parameters to make sure it is consistent everywhere you use it, and then if you want to change it later you only need to change it in the parameters once instead of everywhere it is used across your events).
To actually use a filter, you need to use the Plugin Command Create Godray Filter, etc. There is one plugin command for create / edit each filter type, and there is one plugin command to remove a filter which can remove any filter type.
If you are just using a one-off filter (you won't re-use its settings elsewhere), you can set up its properties directly in the plugin command. If using your preset from the plugin parameters, you can type in the preset id and it will use those settings instead.