This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate. 

As you note, the reference to "Contract Work Hours and Safety Standards-Overtime Compensation" as inapplicable was removed from FAR language.  Yet FAR Clause 52.222-4 is inapplicable per FAR 13.006(e). 

The important thing to note is that this means the Government cannot use this clause or the statute to require payment of overtime.  It does not preclude the contractor from paying overtime if that is its standard practice.