A new Quartus Settings File (.QSF) assignment is available that prevents the automatic packing of the register and its driving LUT into the same ALM. This allows the router to add the necessary hold fixing wire directly in front of the register and does not negatively affect the setup critical path through the LUT itself.
In order to prevent register/LUT packing, use the following assignment:
set_instance_assignment -name QII_AUTO_PACKED_REGISTERS OFF -to <inst_name>
This assignment is available in the Quartus II software version 14.0 Arria 10 edition and later. Future releases of the Quartus II software are scheduled to handle this automatically.