GSX doesn't do any assumption about the location of the Community folder.
It checks the InstalledPackagesPath line of your UserOpt.CFG in the MSFS settings folder, which is the only official method to have whole "Content" ( Community and Official ), moved in a non-default location so, if you use this, it will surely work with GSX.
What's important, the MSFS Content MUST be on a drive formatted in NTFS, because the GSX installer will need to create Symbolic links in the Community folder and for these to work, the drive must be formatted in NTFS.