Filters are ignored when drawing to a RenderTexture. I do not see how that would make objects appear trimmed, but it would likely result in output different from what you are expecting to see.
To avoid this you can use a MeshEffect which does the same as the filter; in the case of ColourMatrixFilter this is quite possible and it has been done before by others. E.g. here is an extension that does something similar in a MeshEffect.