The only two real advantages I can think of that the in-game store delivers compared to third party alternatives is the fact that you can update content while in the game. Probably not the best idea to tamper with game files while the game is running… The other advantage for players on Steam, is that they can use Steam wallet funds.
But I cannot think of an advantage that other stores don’t deliver. Rant below is written from my own experience, which is mostly with Orbx and Contrail.
You want quick updates? Buy straight from developers. Even partner stores like Orbx update faster than MSFS.
You want ease of installation? The in-game store offers this, but the content manager fails to update packages in my experience. Thus you have to uninstall the package and reinstall it. Other stores offer this as wel with apps like Orbx Central, Contrail and Aerosoft One. With these, the installation is as simple as a click of a button.
Maybe you want customisability? I’m not sure what other stores offer this feature, but I know Orbx Direct and Contrail have a configuration menu for some of their sceneries, where the developers support it. This is lacking in the in-game system.
Access to manuals? Once again, offered by the apps from Orbx and Contrail, lacking in the in-game store. I did hear something about manuals in the latest Q&A. Fixed soon perhaps?
The two apps I’ve been mentioning allow you to install the products in a folder outside of the Community folder. They then link the addons with a shortcut to the Community folder. Using an app like the Addons Linker you can then disable them, without having to uninstall them. Which I believe is a feature offered by the in-game system? I haven’t tested this one however.
In short, completely agree that the in-game store is in dire need of some love. In the meantime, I’ll stick to third-party sellers.