Shorter transmission lines or nearer high frequency bypass caps
If it were me, I would slide the FPGA in order to meet the manufacturer's recommendations for decoupling cap replacement.  You have control of the routing from the header to the FPGA.
I think that's an easier problem to manage than trying to do a full up PDN (Power Distribution Model) of your FPGA with the decoupling caps placed in a non-optimum location.