What makes you sad in the MCU GCC options?
The -mfpu=fpv4-sp-d16 is just selecting the FPU for the Cortex-M4 (ARM FPU version 4, single precision only, with 16 double-precision registers). It may also be a MIPS option but here it really is an ARM option.
The differences in the options with those for the Cross ARM GNU Compiler are in part due to the fact that you compiled then for a plain Corts-M4, without the optional FPU, while selecting the STM32F429 for MCU GCC selects the proper FPU. A few others are needed for the ST-provided firmwares to compile correctly (like the weak and packed macro definitions or the various -I options).