I built these this year at the new house. I drilled through the shelf and used a nut and washer on the all thread. On the ceiling portion I used a Sami lag bolt which allows you to screw your all thread into.
Can't say I'd recommend removing any material from the bottom chord of a truss.All I did was predrill a pilot hole into my truss, then screwed in the lag bolt. As far as the size of all thread I bought 3/8” I believe. My trusses run parallel to to my shelves, so just has to make sure I had one near the edge of my shelf. Those shelves are 24” deep, some sections are 10’ others are 8’ in length.