The shape of an airframe in flight is not he same as on the ground; the airframe twists and pulls slightly; what fit once may not fit now.
The 747 frame flexes considerably, even on the ground, as fuel and freight are loaded. Certain exit doors can't be closed, if left open during large fuel uplifts, for example.
A new design on an initial flight is not intended to do more than prove flight. The flight envelope, including systems use, is gradually expanded in steps as part of the test and evaluation process.
During the second flight of the 787, a minor gear problem developed.
Boeing 787 Has Landing Gear Glitch on Second Test Flight - BusinessWeek
When the initial flights are not about proving the landing gear system, leaving it down makes sense. Why complicate an already critical time with irrelevancies?