The bones should be one of the things that aren't random actually. As other people said, you get 6 when you complete the Burial mounds quest (which, by the way, once you know what to do can be completed very quickly, within the second day or even the first I think), and you can get another bone when you complete the specific quest for your chosen upgrade tree (the one that fulfils the Disciple quest), plus one each if you complete Geothermal and Fast Build.after replaying multiple times I can say that it almost feels random, which side quest gives bones. The author seems to like random chance. :/
If you don't mind cheating you can use a save editor to give you bones.You must be registered to see the links
(note that the rewards of the enemies are instead pretty much random; the rewards of searching some of the places, like for example cutting wood or getting scraps in the old world scene, are random but you have more chance to get additional items if you have a higher admiration from a specific captain)