Keep copy/paste and TOC in PDF converted from ebook?
I suppose the first thing would be to investigate Calibre's PDF output to see if it is to spec, and whether it has options that Preview might prefer.
Ghostscript normally should preserve bookmarks and other annotations. Maybe explicitly set -dPDFSETTINGS=/default.?
See the long answer here about using GS:
https://superuser.com/questions/466031/how-do-i-reduce-a-pdfs-size-and-preserve-the-bookmarks
If that doesn't work, you could use this python script, which will copy Bookmarks from one PDF to another. Note that it will overwrite the destination PDF.
#!/usr/bin/python

# Copy PDF Table of Contents from one PDF to another.
# 
# copyOutlines.py &lt;source file&gt; &lt;destination file&gt;
   
from Foundation import  NSURL
import Quartz as Quartz
import sys

def copyOutlines(source, dest):
    pdfURL = NSURL.fileURLWithPath_(source)
    inPDF = Quartz.PDFDocument.alloc().initWithURL_(pdfURL)
    if inPDF:
        outline = Quartz.PDFOutline.alloc().init()
        outline = inPDF.outlineRoot()
    pdfURL = NSURL.fileURLWithPath_(dest)
    outPDF = Quartz.PDFDocument.alloc().initWithURL_(pdfURL)
    outPDF.setOutlineRoot_(outline)
    outPDF.writeToFile_(dest)   

if __name__ == '__main__':
    copyOutlines(sys.argv[1], sys.argv[2])