Open alpha testing of the 5.0 HD mod (online lobby).

1. Could some of the HotA’s generator-related code have unintentionally made its way into SoD?

It couldn’t have.

2. What factors can affect the quality of the generated maps (i.e., how well they match the template): host color, the contents of folders with RMG maps, fix maps, saves, SoD version, connection quality, or something else?

You should ask Sav about that. I know nothing about the generator. I understand it and the templates even less than you do.

All 3 of the 6lm10a generations that I played in SoD with HotA turned out to be incredibly buggy.

To find out who is to blame, we can do the following:
1. Tell me which version of HotA worked perfectly.
(The newer the version, the better)
2. Send me a save file from a buggy generation (you can send several, one save per generation)
3. I will generate the same maps on the old, "good" version of HotA
and if they are exactly the same, then you were just unlucky, and it’s a subjective opinion about "HotA with SoD".
If they are different, then there is a bug.
If there is a bug (although I highly doubt it), then it is most likely in the HW rule 1.38.2, because it affects the generator (to be able to generate mirrors), while HotA doesn’t even come close.
Therefore, be sure to tell me which HW rule you don’t like the generations with: 1.38.2 or 1.40

why have 2 versions, 38 and 40...we need to make 1 working version and that’s it, many people in the game lobby are encountering version incompatibility issues

That’s what will happen. I will integrate the rules into HotA, just like I did for HotA.