I drilled NMO holes and run a STI-CO Flexiwhip for 2m and a 1/4 wavelength Larsen for 70cm. I don't think twice about it, just let 'er run into whatever is overhead. I do keep a 5/8 wavelength Larsen for 2m if I need gain. There is an advantage to running NMO because there isn't anything shear off like PL259/SO239 types. The overall thickness over the sheet metal is maybe 3/4" and then the whips flex above that. I need maybe and inch or two of clearance above the roof.
The Flexiwhip is what a lot of wildland fire trucks run, they are all but indestructible.