I'm also confused about this, particularly as it might be relevant to Barrett Jones. If they want to place a player on IR, is it always like the PS, whereby they have to waive them first? I thought I read during the draft that the team from Northern California often picked injured players (like Lattimore) as their roster is essentially full, and they can get better value by choosing players who would normally have been higher round picks, then stashing them on IR. Do the players they draft also have to clear waivers? Jones, with his smarts and the toughness he showed in playing injured at college, still strikes me as a player who could have a big NFL future at centre, so I would hate to see him lost to a waiver claim before he can establish himself. Can they PUP him without exposing him?
Different rules apply as to when players are placed on IR. Different rules apply to the preseason and "in season" designations. For starters, the PUP list is for players who are injured prior to, and are unable to participate in training camp. Therefore, neither Pead or Barrett Jones are eligible to be added to that list.
If Jones is left on the 53 man roster, and then at some point is deemed to be placed on IR, they don't have to expose him to waivers prior to placing him on IR. In Pead's case, as "X" explained, it was as a precursor to getting to the roster limit of 75 come Tuesday.
They do this to prevent teams from stashing players away on IR, who were "injured" prior to the season starting, therefore never making it to the 53 man roster. Otherwise, teams can "find" injuries to players without ever having to expose them. In the 49ers case, drafting players who never practice, can be placed on the PUP list, and once the season starts, assuming they never participated in training camp, can then be converted to the IR list.