I just spoke with technical support on the phone.
According to the manufacturer, the pipes are secured by fully inserting them; they basically snap into place. Fixing them with screws is not necessary. It is not currently considered critical for the system in its current state because there is a filter in every air inlet that prevents dust from entering the system at all. It looks different when cleaning the system. Special tools are used here which no longer fit into the pipe because the screws are in the way. Additionally, the system is designed to be neutral (surfaces, odors, etc.). The galvanized steel screws simply do not fit into the concept. Not that you would smell them or anything like that, but they now represent a potential weak point in the system. As expected, it can only be somewhat concealed (cutting off the screws), but that does not undo the issue.
I need to sort this out for myself first and consider how and when I will bring this up. The goal should be to enable future cleaning (so cut off all the screws) and cover the slightly increased risk of another damage event (e.g., screw stubs beginning to corrode). The technician said that any form of chemicals has no place in the pipes, regarding the topic of "sealing screw stubs with resin."
Really annoying stuff :-/