I've used both for a long time now. No problems.
HOWEVER: GSX installs in it's own folder and creates a link to itself in the Community folder. I have left it this way, and it is always active when I fly. Addon Linker shows it as an "External link". It is not available in the selection list on the left so I can't disable it like my other addons.
When I fly GA, I just don't use GSX and there are no performance or other effects on my flight.
When I first got GSX, I did change the links for it to addon linker managed links. I found that the occasional airline flight started without GSX was more annoying to me than flying a GA flight where GSX was linked but not used (no noticeable difference). It seemed to work fine when set up this way, but it was a much older version of GSX. The current version might behave differently.
For the record, I also leave Navigraph navdata and navdata base installed in the Community folder and use the linker to select and de-select the Navigraph in-game panels.
