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There will be no problem in setting VDDD, VDDA and VDDIO to 5V in internally regulated mode. VDDA can be as high as 5.5V and for any other pins (VDDD, VDDIO) it should be less than or equal to VDDA.
You can also power the device in externally regulated mode, that is, by directly powering the VCCD and VCCA pins. In this configuration, the VDDD pins should be shorted to the VCCD pins and the VDDA pin should be shorted to the VCCA pin. The allowed supply range in this configuration is 1.71 V to 1.89 V.
Please refer to the section 6.2 Power System for more information.