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Yes, resources created in the VPC will use the DNS servers specified in the DHCP option set, regardless of what is configured for Route 53 Resolver, unless the choice of DNS servers is overridden in the local configuration of the system, such as in the resolv.conf file of a Linux machine.
The Route 53 Resolver configuration only determines behaviour for queries that are sent to the Route 53 Resolver. The DHCP option set controls whether the systems use Route 53 Resolver in the first place or if they send their DNS queries to a different DNS resolver.
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Completely agree with Leo.