Yes you have right what gives page numbering. What I want with the configurable lines and characters per page is that for my custom Kindle settings I could compare books, how much "Kindle Pages" it has and a better way instead of locations, where I'm in the book and how much turns are left from a chapter.
That is ok that you don't feel these optin neccessary or that these option is not good.
By the way I'm happy that the parser will be more accurate in the future.
For my needs I have made some changes in your APNX Generator GUI plugin if you don't mind.
I have added the apnx.py from Calibre source with my custom settings into your plugin and modified to call the APNXBuilder routine from the apnx.py in the plugin rather than from Calibre built in kindle interface plugin.
The result was what I expected!

With my custom settings I could create an apnx file where was just a few pages differece per 100 kindle page turns.
Now I can see that how long (how much kindle page turns) is a book and how much turns left from a chapter to finish the reading and go to sleep.

So I made it.
Thanks for the plugins! And I wait to a more accurate parser.