Hi Guys!
Unfortunately the factory rack will not fit under a 4 panel overhead door.The clearance for such a door is 77" depending on whether or not the garage is equipped with quick turn bracket rails on the door and how the builder framed the outside opening of the door.If you have a 5 panel door the door can be adjusted to allow the factory rack to work.
If you take off the factory rack you need to get the six plastic plates that go over the mounting ports in the roof and don't forget to take the water seal washers off the rack and reinstall them on the little posts molded into the roof.
I have the clearance issue with my garage and ordered a Gobi rack. They make a model called the "Stealth" with an advertised clearance of 76".I spoke to a fellow named Paul in their engineering dept. and he said the clearance is actually 75.5" with the factory 17" rims and stock tires.The Gobi has a weight capacity of 300lbs. and is 84" long.It comes standard with an aluminum wind fairing and front and rear light bars.The light bars are made to accept PIAA 1500XT lights which will fit between the rails of the rack and will not add height to the installation. The bottom of the rack is a perforated steel plate floor.The price is a hefty $1599 delivered

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I find it positively stupid of Toyota to design a roof rack that is too high for 90% of the garages in the US.In addition the stock rack has a minimum of space as the forward section is unusable.
Can't imagine what was on their mind.In addition the radio antenna is also too high for a 4 panel door.Pep Boys has a replacement 16" for $8.99 that works well in my experience.
Marc