A lot of what you're asking for is far beyond the control of UI modding in EQ2. In general, if it seems like something should be an obvious improvement but none of the major UIs are doing it, it's because we can't. Some general comments:
Any filtering of the effects/maintained window is not possible. The game decides what effects you see, not the UI. Bug SOE to change it, but GL, we've been asking for it for years.
Raid window: Much of the stuff you want here you should be able to do. Also IIRC you can already change how the raid window stacks, just resize it...
Player window: Hardly irrelevant because the player is *not* part of the group window. Unless you're in a raid, it's the only place to see your own hp and such. But if you don't want to see it, you can always hide it, all windows are capable of being hidden if you don't want it visible.
Targets: should all be doable. can change the location of one using an event handler of the other (there is no "locking" windows together in EQ2's UI, just moving them via scripting).
Bags: I doubt this is possible, but not 100% sure you're talking about with "joints." In either case, because all bag windows are clones of the same underlying window scripting it to move them in relation to each other may be difficult if not impossible. Depends on if you can directly address the various clones (which I've never tested).
As for buttons to turn windows and such off, such a window could be made relatively easily but the game already has hotkeys to turn windows on and off. I know I don't see the need for it in Fetish, but if it's something you want you should be able to make a custom window that has buttons to /show_window and /hide_window various windows.
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