Doing heavy squats and deadlifts when you have a knee issue is not rehab friendly. A 5x5 routine is focused on heavier weight lower rep. That's the opposite of technical lift training which should be lighter and focused on good form.
It's outdated because it's focused on using barbells with technical compound movement lifts of heavy lower rep range. It's very strength focused, not hypertrophy. OP is in a good rep range for hypertrophy.
If OP hasn't reached a plateau, it's okay not to squat or deadlift. Targeting multiple muscle groups at once is a strength thing.
I have been rehabbing my shoulder and speaking to friends with similar shoulder issues.
One of the better guides we have found was this guy: https://youtu.be/4Gli-tybcyw?si=6NwRkgrxFOXRZ641
His general approach is very cautious. His big issue is giving the tear better conditions to heal. Putting the arm in a sling whenever you can immobilizes joint and takes the pressure off the tear. Then strengthening the traps will fix things more than rotating the arms under load - because the ball of the joint will sit higher and more centred in the socket putting less stress on the tendons.