The way the process works is that the player is waived and then he reverts to IR. The reason for this is because if you put the player direct on IR he counts towards your roster limit and if he clears waivers he does not. This is why the Giants waived Ballard never thinking a team would pick him up and its why New England wont put him on IR until the season begins. Once the year begins all these non-vested guys can go straight to IR without issue.
Players like Baker all have split salaries. He will earn $288K of his $465K base while on IR. Typically all low draft picks (I think rounds 3 thru 7) all carry a split at some point. Definitely all UDFAs do. There are different characteristics of the split that typically have to do with where drafted, but its common.
An injury settlement is paid out based on the full salary for games expected to be missed. So if a player is going to be out for 16 games it would be very rare for the team to have an injury settlement, especially if the player has a split since (as far as I know) the settlement is based on regular salary.
While it stinks for someone like Baker who was probably going to make the team for others it can actually be a blessing in disguise. It maintains a players position on the roster and they can show the team how hard they are working on rehab, learning in team meetings, and doing other things around the facility. Danny Woodhead might not be in the NFL today if he didnt land on IR a few years back. It kept him on the team and made them take notice enough to get him on the PS the next year and a contract the year thereafter.