Looking at the dialog again it says "Do you want to rewrite your 'sources.list' file anyway?" not "Do you want to rewrite every sources file in /etc/apt/sources.list.d/ file anyway?". So I think it is surprising that this had the effect of running with --allow-third-party.
Looking at the dialog again it says "Do you want to rewrite your 'sources.list' file anyway?" not "Do you want to rewrite every sources file in /etc/apt/ sources. list.d/ file anyway?". So I think it is surprising that this had the effect of running with --allow- third-party.