I went thru same problem. Let me explain.
In original user.config.json is SataPortMap; "1" and DiskInxMap: "00"
When I run command sudo ./rploader.sh satamap now I got this: SataPortMap; "5" and DiskInxMap: "00" what is not correct because I got error when says something is error on hdd (2, 3, 4, 5)
Ok, then I left what is was on SataPortMap; "1" and DiskInxMap: "00" and when I install DSM it's showing only one HDD but I have 3. (Yes, I check in BIOS and it's recognize all 3)
Then I figure out to put number 3 in SataPortMap because I have 3 hdd, but again when try to install DSM I got something is error on hdd (3)
Next what I did I change DiskInxMap: "00" with different numbers and what this have effect is just changing position number on hhd's.
Example: if iI set up SataPortMap; "1" and DiskInxMap: "13" showing I have 1 hdd on position 13.
On end I put SataPortMap; "2" and DiskInxMap: "00" and I got 2 hdd showing in DSM on position 1 and 2.
I did't have luck to install DSM with all 3 hdd but it's ok for now I'm happy how works.
What is annoying every time when I play around SataPortMap and DiskInxMap in user.config.json i have to build the loader from beginning and that's so so annoying instead only to change that in user.config.json and save it. If u asking me how I now, I did try to change that and have no effect at all. So only way is to have to build the loader from scratch.
If someone know better/easier way please let us know.
Bu the way "pocopico," made great job making script/loader and I want to thank you so much.
Cheers