First, it is important to note that neither AS9100 nor ISO 9001:2015 require a procedure for “time clock policy and procedure”, so there is no direct requirement telling you to create this document. Additionally, not every procedure needs to have a direct link back to AS9100, but if you choose to do so then you can certainly include this information.
I am assuming that the previous reference for ISO 9001 clause 6.3 is from the ISO 9001:2008 standard where this clause is about infrastructure because the ISO 9001:2015 version clause 6.3 is about planning for QMS changes. If this is the case then the new standard, both ISO 9001:2015 and AS9100 Rev D uses clause 7.1.3 for the infrastructure requirements. However, depending on the content of the procedure clause 7.1.2 might be more appropriate as this is the requirements around people resources.
To find out more on what is required in AS9100 in plain English see the whitepaper: