There is a couple reasons for this in my opinion. First: no matter how good you are, you'll never get the wood cut to perfectly match the hull. This can leave hard and soft spots along the line of the stringers that can reduce structural integrity. These spots are weak points that can cause flex and lead to tabbing delamination. If you plan for a gap, your cut doesn't have to be 100% perfect. Second: you want to ensure you properly glue these structural components in place. Leaving a 1/4" gap between the structure and the hull ensures a solid attachment of the structure as you push thickened resin under it. I like to add chop strand to my thickened resin for more strength and protection against shrinkage cracks as the resin kicks. Third, (and I have not heard anyone mention this): added protection against water intrusion. Boats rot from the bottom up. If the wood sits against the hull, any tiny bit of water will eventually get soaked into it. If you leave 1/4" gap and pack that gap with thickened resin, the water has to be atleast 1/4" deep before it touches the wood. You'll add fillets to the structure to properly tab it to the hull. If the wood is against the hull, the fillets will create a trap for the water, helping to channel it into the wood. Water in wood equals rot. Rot equals unhappy boaters.
Bottom line, bedding the stringers with atleast 1/4" of thickened resin is the right way to do it. Manufacturers do not take the time or extra effort to ensure this happens. Take your time and do it right, paying attention to all the little things. Ensuring structural integrity and water proofing wood components is really the most important things you can do in a restoration.
