Yes, the planes are flown by test pilots. For the big Boeing and Airbuses they go through process similar to a user acceptance test. Once the manufacturers test pilots go through their checks, representatives from the airlines will form a punch list of items to be fixed before they accept delivery.
As a side note, 787s out of the Charleston plant are known to be problematic, airlines don’t accept planes from that plant without significant inspections.
For smaller manufacturers like Cirrus and Cessna the process is similar. They will all be test flown, all of the engines will be test run, and the buyer gets a report. You often hire a pilot to ferry the plane from the factory (that is a real pilot job, ferrying recently purchased planes to their new homes) and part of that pilot’s responsibility will include inspecting the plane.
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