A good number of BIOSes have trouble booting from GPT in non-UEFI mode. This is commonly reported with Lenovo laptops, including my x220, as well as a number of Dell servers. Although UEFI is the preferred boot method, a user may wish to boot one of these systems via BIOS/CSM, and some systems (such as an AMD FX-6100 I have) fail to boot via UEFI from our GPT memsticks.
The "vestigial swap partition" was added in rS265017 to work around an issue with loader's GPT support, so we should not need it when using MBR.
There is some concern that future UEFI systems may not boot from MBR, but I am not aware of any of these today. We can revisit this change if this becomes a concern in the future, likely returning to GPT for the main case and introducing a separate MBR BIOS/CSM-only memstick.