Yep, this is a front office philosophy that predates Dak and likely will continue after him, considering the Stephen Jones will be running the team. As has been written multiple times, it goes back to overpaying Brandon Carr and him being a good but not great player. Carr was kind of the last straw for the staff, other players like Marco Riviera contributed to the philosophy change.
Dak's $90 million for this year probably wasn't included because we don't know what his actual hit will be. His contract was set up for the base to be restructured this year, creating quite a bit of cap space.