What the crt shaders try to do is a little bit of blurring and scanlines at the same time, to overcome the limitations of bilinear filtering. But the shaders are too intense for the pi to run. So, one has to make a choice between accurate scanlines, a smooth image, or a smooth image with inaccurate scanlines.

Personally, I think the inaccurate scanlines of the bilinear filter image look as bad as a misaligned scanline overlay and are very distracting, but some people might not be bothered by them.