Does using base: core18 is the snap.yml file affect compatibility in any way when the app is installed in Ubuntu 16?
I believe the short answer is that the base should not affect compatibility with the system that the snap is installed on. If you are seeing compatibility issues, that would sorta imply to me that your snap in incorrectly configured.
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On places where the snapped application will directly accessing resources from the host, compatibility issues may occur and make some functionalities not working properly, for example like input method frameworks and fontconfig.