1. Unfortunately, yes.
2. There are flash algorithms for programing of external QSPI flash memories. This is supported by both CodeWarrior and S32 Design Studio. The algorithms are provided by Pemicro.
For my surprise, I found out that S32DS does not support MPC5645S (only this one seems to be missing, other MPC56xx are supported). MPC5606S is supported by S32DS. So, it will be necessary to use CodeWarrior for MPC5645S.
In both IDEs, you can select alternative flash algorithms (*.pcp files). Search for "spansion" keyword in installation folder. Names of files contain supported memories.
Regards,
Lukas