They should not have hacked out the fascia or guttering, but a riveted patch would be an ample fix. Water ponding will occur in 90% of homes, especially over time with building or roof movement, build up of leaves, dirt, pigeon poo and other debris, so a minimal layer of silicone is a very minor issue.
I wonder if these A/C people really know what they are doing here. The pipe is a drain for condensation that can collect in the R/C A/C roof unit, and not to be confused with an evaporative A/C pipe that periodically dumps its water when it becomes salty etc. Its this salty water that will stain one's roof and corrode the guttering, necessitating siting it over a downpipe, because its easier to replace a rusty downpipe than guttering.