If the skylights are curbed rather than flush to the roof yes a metal roof can be flashed around them and metal roofing manufacturers should all have instructions for doing so.
How to install steel roofing around skylights.
How to roof around a curb mount skylight.
Install 6 in wide strips of a self sticking waterproof underlayment.
Weave the step flashing up the side of the skylight as.
This underlayment will direct any water that may get through the metal flashing onto the roofing felt.
Steel roofing can be costly but it is a lifetime investment.
Secure by nailing the flashing to the roof.
For those who are unfamiliar with the term flashing it is a thin material usually galvanized steel that is used to direct water away from certain areas of the roof.
Repeat to install the flashing to all sides of the skylight frame.
Even the best skylights have only a 20 year warranty.
Then fold the tabs on all sides of the skylight and screw them down.
Before you install metal roofing repair any damage to the wood under the shingles.
However the way your roof is flashed against the skylights will be one of the most crucial aspects of the installation process.
Galvanized steel which is created by using a soft layer of zinc to protect the inner layers is the most common type of steel roofing.
Next use 1 inch nails to secure some metal edging to the perimeter of the roof.
Install from the bottom up lapping each piece on top of the lower one.
Then cover the entire roof with a layer of insulation and secure it with a staple gun.
Once the metal flashings are ready place the pieces between the roof and skylight above the roof and under the skylight.
Noise is usually not a factor if you are installing a steel roof over asphalt.