For example, Boeing might specify the landing checklist to consist of gear and flaps only whereas the airline might add cabin secure, speedbrake armed, missed approach alt set etc.
Absolutely true (and this is part of the business model, because this costs money).
On the subject of callouts: (FCTM) "Recommended callouts are provided in the interest of good Crew Resource Management. These callouts may be modified by the operator."
However "Recommended callouts differ from procedural callouts found in the Procedures section of the FCOM.
Procedural callouts are required". So I would be really curious to see if Boeing these days still approves that procedure, and how much freedom airlines still have these days.