First of all – and I am glad to see your article makes this clear — there is no difficulty with specifying hard stanza breaks and hard linebreaks when formatting EPUB and MOBI files.
The problem arises — as pointed out in the example used in your post — when lines are too long for the screen. This could be because they are just really long lines; or because the reader has chosen to enlarge her e-reader font so much that the lines no longer fit on the e-reader screen. In either case, the too-long line will wrap to the next line, hard up against the left margin. It will look both wrong and untidy.
What do print publishers when a line is too long for the page? The resolution for e-publishers in this dilemma is the same as it is for print publishers — the hanging indent.
There is a poetry collection here (http://bit.ly/hSOG43) and a chapbook here (http://bit.ly/ht3Ydv), both of which have been formatted using the hanging indent – which involved essentially formatting each line as a *potential* hanging indent paragraph. You can download these e-books either as EPUB or MOBI files (as you know, the two e-formats that together support most popular e-readers). I invite you to do so and test them on your e-readers. In both final e-formats, the lines wrap with a hanging indent *if* the font size used makes a line too big to fit on the screen, but appear whole on one line without indent if the font used is small enough for the whole line to fit on the screen.
There are other, real problems with e-book formatting for poetry, but they are not those identified in your post.