Showing my ignorance here, but what is the best way of obtaining a
file from a .svg file done in Inkcape, while preserving transparencies
and true colours?
You can't have transparency in JPG. It's not supported by the format.
Use PNG or GIF if you need transparency. In any case, PNG is much
better suited for the type of graphics that Inkscape typically
produces (sharp boundaries, flat color areas). JPG is not efficient
for such graphics and introduces ugly artefacts at boundaries.