Well, of course what you are asking is not possible, because it will just broke Seated passengers. and it doesn't seem you fully understand what the GSX Installer does or what the layout.json file does.
I have many options changed on my layout.json files (for FTSIM+ Sound packs for example) and every time I open the config menu of GSX the layout.json of all my aircrafts will be overwritten.
Let's start from the back: it's not true the layout.json of "all" your aircraft is being overwritten. ONLY the one for those who support Seated Passengers AND you have enabled them.
But that's not really the main point here. Your usage of the sentence "will be overwritten", seems to assume you think we overwrite your file with some canned pre-made version that is only valid for GSX, which is not obviously the case, the installer is not that dumb to just assume a certain layout.json that wouldn't take into consideration OTHER changes in the package, including those not made by GSX.
I hope you know what a layout.json is: it's not something you edit yourself, it's supposed to be the exact picture of the content of the package folder at any given time, to inform the sim of all files in it, with their size and date, so you add or remove files to the package, you must then regenerate the layout.json automatically, I guess you use the popular MSFSLayoutGenerator.exe to do that.
Well, that's EXACTLY what the GSX Installer does, it recalculates the CORRECT layout.json based on the actual package contents, exactly AS IF you would do it manually when you used the MSFSLayoutGenerator.exe to add your own changes to the packages.
This means:
- If you added/changed files to the package before using the FSDT Installer, the new layout.json that will be overwritten by GSX will INCLUDE your changes too.
- If you add/change files to the package after having used the FSDT Installer, if use MSFSLayoutGenerator.exe to update it, it will INCLUDE GSX additions as well.
So, in either cases, both files will be valid, and you don't have anything to worry about.