"I have a 75 year old brick row house with a flat roof. Rubber roofing
was installed about two years ago and is intact, with no apparent
problems. There is no attic.

Of 6 proposals I have had to install central air conditioning, the most
attractive is one that will put the unit and much of the trunk ductwork
on the roof. This will require the roof to be penetrated about 5 times.
The contractor has a roofer who will flash and seal everything once the
ductwork is completed, but I have an instinctual fear of perforating
the roof.

Is this an invitation for trouble? Can water flow and seal be done
effectively (the roof pitch is very low). Should I bring in my own roofer?

Any thoughts or discussion will be much appreciated. "

It's standard practice in commercial work.

Usually the duct support legs, if any, come down in pitch pockets, which are flashed into the roof, and the duct penetrations run through low curbs, which are flashed and counter-flashed.

The curbs are typically 6 to 8 inches high, and the rubber roof would run up the sides of them and be fastened on top. Then a metal counter-flashing would be attached to the duct, and extend out over the top of the curb and down the side a bit. Usually angled cant strips are installed at the base of the curb, but this may not be necessary with a flexible rubber roof.

Done correctly, it's trouble-free.

If you liked your roofer, and want him to be fully responsible for the roof penetrations, by all means use him to do the work.

Rubber roof is fairly easy to flash, using the rubber amterial and adhesive.