From my look into the issue, my personal impressions:
1. it is simple PDF and there seems to be no file based georef structure
2. yes, this function needs to be open (if it is not yet, still digging into it)
3. no tool whatsoever needed, the only thing is a ruler
Skydemon uses a simple one page standard PDF and puts information in a index.xml on where on the page a box to display is, how tall and how wide the box is and then a list of reference point on the basis of x,y position on the page equals latitude,longitude.
Yes, I would welcome too, if some standard would be used, such as a Maptiles structure or GeoPDF, but so far it looks as if Skydemon goes the easiest way out - which is fine, because switching all aviation agencies to deliver GeoPDF will not happen during the next years, or millennia.
Btw, how do I add User Documents for a field with ICAO denominator EGXY in Skydemon PC Plan? I tried to use the Textual Information button in Data Creator, but always get a 'No textual information plate was found for EGXY' error.