[GeoffR]

Publishers should allow for the fact that the reader can adjust things like spacing between paragraphs, set full-justification or ragged right, etc. (either by a setting on their ereader, or by editing the book's stylesheet.)

So alignment for the main text should be left undefined so that the reader can choose full-justification or ragged right themselves. Of course titles, chapter headings, and other text that shouldn't change when the main text alignmant changes should be set by the publisher.

Scene breaks should be indicated in a way that allows the user to change the spacing between paragraphs without losing the scene breaks. I.e. indicate a scene break with a special symbol (* * *, etc.), or by capitalising the first few words of the scene, or using a drop-cap, etc. That way the scene break remains visible if the reader changes the paragraph spacing.

Edit: If using space alone to indicate a scene break, at least add the space as padding rather than margin, so if the reader chooses to add spacing between paragraphs then the scene break will still be visible as an extra space.