A bit late but as far as I understand the question, you want to ensure that only visible layers are rendered during processing because your file has some invisible or hidden layers which re-appear. Since iText support will not help you, there is another (free/GPL License) way.
The first step is to 'burn in' the state of the layers and remove the optional content while honoring the visibility state, using another processor. Once that step is done you can continue with whatever version of iText you want.
There are 2 processing options that can 'burn in' the visibility state of Optional Content Groups (= Layers = OCG)
Option 1
Use www.ghostscript.com with -sDEVICE=pdfwrite command line. See GS documentation for full command line
Option 2
Use Poppler's pdftocairo.exe with -pdf command line.
Both will create a PDF that has no interactive layers, with OCG removed. All iText operations will work as normal on that file.