don't edit the apt.dat file... instead, maybe try using the NavDat override capability...
in your "myflightgear/myscenery" private scenery directory, create a directory called "NavDat"... inside that one, another directory named "apt"...
~/myflightgear/myscenery/NavDat/apt
now, in the above directory, create the file KLSV.dat and copy the contents of the KLSV section in apt.dat into the file... make your edits and then start FG...
~/myflightgear/myscenery/NavDat/apt/KLSV.dat
since you should have FG already looking at your "myflightgear/myscenery" directory for your custom scenery, it will also look there for this NavDat override... if it works, FG will rebuild the navcache file when it starts up... this will appear similar to what it does when you upgrade from one version to another... you should be able to see evidence of this rebuilding as well as the inclusion of the KLSV.dat file in the FG log file...
once you have the position figured correctly, check on the x-plane gateway and see if it is the same there... if it is not, maybe submit a change there so it can be included in the next apt.dat update and scenery build...
the only other thing i wonder is if the tower height is based on AGL or ASL
"You get more air close to the ground," said Angalo. "I read that in a book. You get lots of air low down, and not much when you go up."
"Why not?" said Gurder.
"Dunno. It's frightened of heights, I guess."