This is handy some of the time, and others, just really frustrating.
All too often, when I really need a well formatted PDF, I just have to resort to using my Mac, and the Export command in Safari.
I think Readdle has done all they can within the limits of iOS, but be aware that its not a given that youll get satisfactory results.
Atavachron about PDF Converter by Readdle, v2.3.4