Well, after some tests, final conclusions about the margins hack (jar edition) in PW1 6.5.1.1:
The edited margins work "almost" fine with azw3, they don't work with mobi:
1. In mobi books, you can set the new margin but it is reverted to the default one (the small default one, 50 pt or close) every time you turn the page.
2. In azw3 books, if you set the new margins, they survive the page turn, but they don't survive a return to the home page. Once you change the book, or even without opening a new book but exiting the book you are reading to the home page, when you return the margins are lost and the default (small one) is set.
That is, in azw3 you must set the margins for each book, which is more or less acceptable. In mobi, you must do it for each page, which is "a little bothering"
When the margins are "automatically resetted" by the kindle, they are the same as shown in the home menu, view list. Maybe the key could be to modify also those, but I am not willing to follow this research. I just mention it here in case it could be helpful for someone in the future. I will copy these conclusions in the
JBPatch thread, where the margins are also discussed, for the same reason.