Hi rshipman ,
Please read these document at first, I think you will be more clear about it:
1. RT1020 flashloader:
https://www.nxp.com/webapp/Download?colCode=Flashloader_RT1020_1.0_GA&appType=license
i.MX MCU Manufacturing User's Guide.pdf located in folder:
Flashloader_RT1020_1.0_GA\doc
You will find these information:

the version is the HAB library version.
2.Security Application Note AN12079
From this AN, you will find signed is using the 4.2. 4.3 is the encrypted mode.
Now, answer you questions:
1). Why are they different?
Answer: yes, different HAB version, and different mode, signed is signed, secure is secure, please check the AN12079.
2). Where do we get this version from?
Answer: it used to choose different HAB version, you don't need to know more details about it, you just need to know how to use it.
3). Or what should we be setting to?
Answer: You can refer to the AN12079 to do the detail settings. The flashloader also give the different bd file, you can read it, it will be more clear:
Flashloader_RT1020_1.0_GA\Tools\bd_file\imx10xx

4). Is there a document that describes the difference between 4.2 and 4.3 etc?
Answer: please check the AN12079.
Wish it helps you!
Have a great day,
Kerry
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