I hope I have to understand well. I think you cannot have this kind of fine control on page breaks on PDF produced from an Excel template due to the nature of Excel that is not designed to produce well formatted PDFs but to create analysis models.
If you insert a page break in a Qlik NPrinting Excel template level only the first page break will be copied in the final report right now (June 2017). Following page breakes are not copied (2nd, 3th, etc) as it happens in Word templates.
So if using Excel is mandatory and charts do not always have the same height I think the only solution to have a fine control of the pages layout is to:
Remove the level
Insert a copy of the charts you need into the template for each value of the fiels in the level
Add an object filter in each chart
Control each chart dimensions by setting its properties
Insert pagebreaks exactly where you want the break
Use the Excel PAge Break Preview to fine se the pages
Of course this solution is very long to be implemented and it is feaseable only if the number of distinc values in the level is limited.
The suggested template type to get high quality and control of the output in PDF is PixelPerfect.