Good point. Seems I have always misinterpret retention/endurance specification a bit. But the graph you pointed out clearly shows data retention specification apply to all blocks.
For larger blocks there is limited maximum endurance (number of erase cycles), but data retention for data stored in certain block is given by number of erase cycles performed before that i.e. it is independent on used block.
So question staying open is why "EEPROM should be avoided for storage of executable code". In my opinion there is not reason for such statement with MPC5777C and MPC5746R where ECC error reporting may be enabled so I believe the note is relic from previous documentation and should be removed.
Let me check with the factory, I will return to you as soon as possible.