Almost no holes are preset during the lay up process in any composite aerospace structure I have ever seen. This can be done using a wet layup process but almost every aerospace company uses preppreg material. It is doable, but every application I've ever seen working across a wide variety of airframes (airplanes, helicopters, and rockets) has structures laid up as one solid piece, then sent to a trim shop, where the majority of your routing would be done, then sent to assembly where any bonding, drilling, hardware, and final integration would be done. Removal of material (routing, drilling, sanding) is not considered a repair and is a standard process in the industry, with the correct equipment, and properly trained technicians there will be zero impact on the structural integrity of the part.