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Doesn't getaddrinfo respect /etc/resolv.conf? So LittleSnitch should install itself there if it wants to be used by getaddrinfo.

Besides, apps can always make direct lookups to a resolver of their choice, bypassing any resolver hints of the operating system.

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The /etc/resolv.conf system is woefully inadequate. It doesn't have a concept of per-interface customization so you can't customize according to the currently active network interface. It doesn't distinguish between DNS configuration delivered by the network administrator (which can and should be changed remotely) versus set by the computer administrator. It doesn't work very well with VPNs where a specific DNS server is used for resolving addresses on that VPN.

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