[Marinolino]

I don't have 13" Sony, but white margins are there IMO because you've been using fit-to-page mode or fit-to-page-height mode in your reader, wherein the shorter page is shown without the margins (both shorter 3.99/5.47 and the longer page 3.99/6.75 are at the same 3.99 inch width).

You should simply choose another reading mode if available, e.g. on Kindle DX (using koreader app) it would be fit-to-page-width or fit-to-content-width, but in that case it would also take two screens per pdf page for the longer 3.99/6.75 page(s).

If you want the page B (shown without margins) to be rendered as with margins, like the longer page A, you can use Adobe Reader's crop function i.e. the change-page-size function therein, or any other pdf editor with a similar page-size function, just quickly changing page size to 4 inch and 6.75 inch height for all pages, also choosing centered page.

It should take less than a minute for the whole pdf.

The shorter page(s) would look like in an attachement.