Looking back at the original question it appears there are two issues complained of:
1) Numbering of pages within the book
2) New page breaks with each "chapter" (component xhtml file)
The reason for breaking the book into separate files, as noted by the OP is performance - the reader only needs to have a single file open and parsed at a time meaning that the total book size is not limited by the RAM on the device. Try building a 2Mb book with a single chapter and opening it on an E-reader with only 512Mb of RAM and you'll see what happens. This is one reason I moved from using FB2 format to EPUB - FB2 is just a single mammoth file and I couldn't get some large books to work because of it.
As only one xhtml file is open at a time the display will of course start on a new display page (the reader has "forgotten" the previous file).
Page numbering is effectively a function of the reader - as noted previously the Kobo now has the option to display either chapter page or global page numbering. This though is a feature of the reader and can't be applied on a book-by-book basis. What I have noticed is that if you have chapter numbering in effect a tap on the centre of the screen will bring up a top bar to replace the book name which initially will display the time of day; if you wait a short time it will change to global progress as a percentage of the book read. Not as good as the old progress graph but a reasonable compromise.
BobC
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