How the organization calculates salaries and hourly rates is an individual decision based on its (past) accounting and financial practice. If overtime is and has been normally paid and overtime is needed for travel etc. then in our view it is a legitimate cost.
Note: many hi-tech companies do not pay overtime – in which case only standard time should be paid. But again there are exemptions to this, where the organization does its costings based on assumed average overtime and all employees normally record all time, including overtime, even if not paid extra for it. In short, the organizations accounting system (existing prior to the project and not altered because of FP6 participation) determines the basis.