Hi,
For the information you are providing, you are using yocto project, is this correct? If so, we are not obtaining the image from yocto project, but from manually building both u-boot and ATF (as described under the AN13750).
Below will be some comments on regards of your questions:
A1 >> They are not the same. Seeing the contents of both fip.bin and fip.s32-qspi, fip.bin is the binary for the fip itself, while fip.s32-qspi contains both the fip itself and the whole IVT structure which can be flashed directly to the QSPI. As seen on the image below, the offset of the image is different from the *.bin (no offset) to the *.s32-qspi (offset):

Again, the offset is due to the IVT structure under the *.s32-qspi file.
A2 >> Can be obtained by manually building both u-boot/ATF. This is described under the "Manually building Linux BSP components" under the respective BSP User Manual, or under the AN13750 itself.
As a note, codeaurora link is not available anymore, the new link should be the one from github itself:
https://github.com/nxp-auto-linux
As for yocto, should be located under the following path:

A3 >> On regards of the RAM pointers under the IVT, they are not the same. The addresses are the following:

This can be confirmed by looking into the *.map file from the Bootloader.bin.
Please, let us know.