Use bootstrap() in pytest where applicable

Use bootstrap() in pytest where applicable

Replace the autouse fixtures which were only used to change the initial
server configuration into proper bootstrap() functions. This gets rid of
an extraneous reconfigure.

In the tests_validation_many_anchors.py, split the fixture into a proper
bootstrap() and a separate test for checking the expected log lines for
the ignored keys. Previously, the test was broken - it should check for
all the messages being present in the log, and some of the keys are
actually initial-key rather than static-key. This has been fixed in the
parametrized test.