I'm a firm believer in NMO mounts for VHF/UHF/800/900 band antennas.
The center of the roof is by far the best place to mount them, because the roofs flat sheet metal forms a ground plane, giving you the best possible omnidirectional radiation pattern.
I've done dozens of commercial radio installations on F-Series trucks, the headliner comes out pretty easy, takes about 10-15 minutes to remove.
You could cheat and not pull the headliner by using a 3/4" mount, which is fed in from the top, but they're not nearly as strong as the 3/8" mounts which MUST be mounted from the bottom. This is the only type I personally use, unless the customer requests something different or supplies his own.
For mounting the radios on these trucks, I usually do them overhead, right above the rearview mirror.
It works great for small units up to 6" wide, such as Kenwood TK-780/880's, Yaesu FT-7800/8800's and Motorola GTX's without interfering with the sun visors.