I have observed windows doing exactly this before in my own PC, it seems to want to stick the boot files on lowest numbered disk that's marked active unless it has no choice.
So the issue here is that your own PC has a true BIOS, which will see all attached disks, and number them in a particular order. The boot order can be selected in BIOS setup, which a PC has. Apple hardware does not. So my guess is that either you had Windows installed at one time on this other SSD. Multiple boot loader code (on two or more disks) confuses Apple's firmware, and that confusion manifests itself differently on different models. Most of the time zeroing sector 0's first 440 bytes, and restoring the hybrid MBR to a PMBR will fix this confusion, and Apple's EFI will exclude GPT only disks from scan. The first disk found to have a hybrid MBR, with bootloader code in the first 440 bytes of sector 0, and with a partition marked active (bootable) will be the one it tries to boot from.
In any case the rMBP appears to be behaving differently. Unclear if it's a feature or a bug.
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I can't believe it but a MBR was created on the internal fat portion see below
I think you're confused. Paste the previous command that created the mbr0.bin file.