The problem is that how a Lily output is rendered by a PDF reader is not within the realm of control for Lilypond. The fact is that some PDF features are handled differently by different viewers, if they are handled at all. For example, in my graphic design work, I learned that transparency is a big issue. Text is, as well. Depending on how a PDF viewer rasterizes the outlines, lines of text can look horribly crooked, Letters composed of horizontal and vertical lines will look thicker/darker than other lines, etc. If I outline the text, the look is fairly consistent on the screen, and it looks fine either way on a 300dpi printed page, but this kind of stuff is going to happen at screen resolutions when the output is intended for print.
As far as what can be controlled by Lilypond and it's developers, making sure PNG files are generated well *is* something that should be addressed, since that is completely within Lilypond's control.
Cheers,