All very useful suggestions. I don’t have any plans to develop this plugin further, but some quick answers work arounds.
Alignment could be controlled in the makepdf.php file after line 194 (the plugin uses the TCPDF engine so the exact setting could be found on that site).
Multiple pdfs – you could do multiple versions by renaming the file on your server and manually linking
Date order – the plugin generates it’s own rss feed using the rss-make-pdf-newspaper.php file. There might be something you can do in here to flip the date order.
Hope this helps