Not familiar with Trilliums but will say that on my
Casita Freedom Deluxe, there are holes in the floor where hoses from the portable water tank, suspended under the camper, came through the floor one one side and drains for water heater and fresh air intake for
battery on the other side of the camper in these cubbies. Someone may have done away with this stuff under the camper and just plugged the holes with tin.
As for the mud flaps, NO it is not normal to have screws into the fiber glass. I did install mud flaps but suspend the home made flaps (out of door matts) off a horizontal rod off the frame.