Hello Francisco,
flex link is enabled on a pair of links and only those pair of links have STP disabled:
>> STP is disabled on Flex Link ports. A Flex Link port does not participate in STP, even if the VLANs present on the port are configured for STP. When STP is not enabled, ensure that there are no loops in the configured topology.
see
http://www.cisco.com/en/US/docs/switches/lan/catalyst4500/12.2/46sg/configuration/guide/swflink.html
So my understanding is that unless you disable STP on a per vlan basis, STP is still running on standard ports including access ports.
If so, you can take advantage of using both portfast and BPDU guard on access ports even if uplinks are on flex links for the usual reasons: no TCN on port state change, safety in case of connection of user provided lan switches etc.
I would suggest that this option should be preferred over disabling STP for selected vlans
Hope to help
Giuseppe