In those cases, why not just have the window manager lie to the application and say, effectively, "your request to position the window at the coordinates you specify has been fulfilled", but actually position the window where the window manager wants?
That way those java apps would still work, right?
And yes, I use i3, so I am a fan of tiling windomanagers too. Not everything nicely fits into such a box though, and it's better err on the side of compatibility here, than say, can't use that app, sorry