There is no real solution to those cases and as you said it shouldn't be
an issue for most users, probably not worth coming up with an hackish
workaround (and the issue is not specific to deja-dup). One other case
of such reports is also an outdated schemas in /usr/local or such taking
over the package version

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https://bugs.launchpad.net/bugs/1712757

Title:
  /usr/lib/x86_64-linux-gnu/deja-dup/deja-dup-
  
monitor:5:g_settings_schema_get_value:g_settings_schema_key_init:g_settings_get_value:g_settings_get_boolean:deja_dup_migrate_settings

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