test: do not run box.cfg{} on test runner for replication tests

Some replication tests (linearizable_test.lua and
bootstrap_strategy_test.lua) used default test-runner to test box.cfg{}
calls which are expected to fail.

Since box.cfg{} is going to be prohibited on default test runner, let's
move such test cases into properly initialized servers.

NO_DOC=test
NO_CHANGELOG=test

(cherry picked from commit 8b10902d)