Twinline Alternative Notation

Does anyone know whether future versions of Musescore will inculde the ability to select and colour individual staff lines and even the spaces in between the lines? (I have found some workarounds but they're not really satisfactory)

No except if someone makes it happen. But realistically, there is no good reason since standard notation doesn't need it.

Can I permanently alter the height where certain notes appear upon the staff? (e.g. Could I move all C#s up off their line and into the D space?) This question seems to be the crux of the issue.
You can move a note to a given pitch, so it sound correct, and then fix it to this line in the inspector.

Can I make certain noteheads permanently triangular? (e.g. All C#s become upward pointing triangles and all D#s become downward pointing triangles)
Not dynamically, but a plugin can be made to change notehead according to pitch, tpc, line or the current weather when the plugin is run (meaning, if you change a note pitch etc..., you will need to run the plugin again).

Can I make certain noteheads permanently be coloured blue? (Seems like I might be able to alter an existing plugin to do this)
Via a plugin, or manually via the inspector.

Realistically, if you are new to music notation, I suggest you learn standard music notation, it's a standard among millions (billions?) of musicians, refined by centuries... and MuseScore's main purpose is to render standard music notation.