Make TlsBypass and PrefixDiscoveryBypassTls non-flaky

The problem was caused by a race between the test code calling
DnsTlsFrontend::clearQueries() after receiving the query response, but
before the server had actually incremented the query count.

Using an atomic<int> for the counter doesn't help us here. A more robust
synchronization would involve a mutex and a condition variable, similar
to how DnsMetricsListener::waitForPrivateDnsValidation() does it.

Change-Id: Id78180f1e168d8385b5f0d711106adee35f146ee