In general, more configurability would be awesome, but I realize that wouldn't be a quick fix.

What do you have in mind? What configurability? I only can have it on or off, and if its off, its casted.

Right now buffomat overrides molten armor with mage armor or ice armor, and molten armor isn't an option--- ideally it'd be an option here:

is it just removing one line?

Wait a second, this is Season of D, and they added molten armor? I stopped following SoD for a few months.
So yes, you just remove :RequireTBC() in AllSpellsMage.lua for molten armor
The spell ID has changed it seems, from wowhead i can find
428741 https://www.wowhead.com/classic/spell=428741/molten-armor
and 409307 https://www.wowhead.com/classic/spell=429307/molten-armor

are you recommending that I put my fork in my Interface/AddOns dir, or would you like a PR upstream to here?

Sadly there's no quick way for me to test this, my mage in SoD is 16 and i don't have plans to level it. Min level for emerald wardens is 23 though, not too far off
if it works for you i'd have either a PR, or a code snippet to paste and commit, but then your name will not be in the commits history :) can put it in the code comment though

I got my fork up and running in my personal WoW build, but Molten Armor didn't show up as an option. Perhaps bom isn't reading the rune tab of the spellbook?

No it doesn't, if the spell doesn't appear as a learned spell, BOM has no idea that the spell is available (and no idea how to cast it, standard macro /cast which BOM uses doesn't seem to work either). I might need some advice how to read that.
It is quite silly, you can use armor slot, like /use Legs Rune Ability but that's not cool with BOM.