First, silk is very fine, has higher tensile strength than cotton or linen. Second, which is probably the real reason, is that it's expensive, so it fits into the aviation business nicely.
You shouldn't need thread around the thru-bolts at the saddles. If that area is nicely lapped and everything is torqued properly, there should be very little leakage into the stud bore. The perimeter is different: it isn't so solid and stiff as the bearing saddles, and simply tightening the small bolts will cause a small amount of waviness that results in leakage. So the manufacturers recommend the thread and sealant.
Now, on this debate as to whether the overhaul manual is mandatory: What does FAR 43 say?
§43.13 Performance rules (general).
(a) Each person performing maintenance, alteration, or preventive maintenance on an aircraft, engine, propeller, or appliance shall use the methods, techniques, and practices prescribed in the current manufacturer's maintenance manual or Instructions for Continued Airworthiness prepared by its manufacturer, or other methods, techniques, and practices acceptable to the Administrator, except as noted in §43.16. He shall use the tools, equipment, and test apparatus necessary to assure completion of the work in accordance with accepted industry practices. If special equipment or test apparatus is recommended by the manufacturer involved, he must use that equipment or apparatus or its equivalent acceptable to the Administrator.
So it's either the "current manufacturer's maintenance manual," or "other methods, techniques, and practices acceptable to the Administrator..."
My opinions or personal shop habits won't be acceptable to the administrator. I would need to come up with my own manual and have it approved. Only a big outfit could afford that sort of thing.