This actually got me thinking... would it be possible to mod AssignStartingPlots so that it reads the values from a new table, instead of having the values defined in the LUA code?
No. I mean, yes, you can have Lua read XML, but that part's not actually the problem.
The first problem is that when the script calls GetMajorStrategicwhatever, the calling statement has a specific number of arguments. It's not being handled as an allocatable data structure or anything like that, so when the calling routine has 7 arguments and the called routine returns 10, or vice versa, then things break. It's just not dynamic; if you add a new resource, then you need to rewrite all of those, and that's what makes it incompatible with, say, the Lakes map script (since it has its own version of that subroutine). If the devs were smart they'd have written the map script resources as a modifier, so that you could default any new resources to x1, but they instead took the cheap way out and overwrote the existing routine. (The fact that map scripts override mods is also backwards, IMO.)
This also means that if you restructure AssignStartingPlots to read from files, then the Lakes, Great Plains, and Highlands map scripts will stop working entirely unless you make new versions of them as well.
The second problem is that the rarities are all handled through a bunch of weighting tables, and while you COULD transfer all of those to XML, it'd be a HUGE amount of work. So if a Small deposit on a grassland hill has a 25% chance of being Iron, a 45% chance of Uranium, and a 30% chance of Aluminum (just making those numbers up), then think about how much XML you'd have to write to just set that ONE rarity table. Now double that for the Major deposits, and add in the other dozen or so terrain types.
Besides just being a tremendous amount of work, you'd also end up with something that's completely incompatible with any future updates. Now, if Firaxis was smart they'd do this themselves, so that they could fix the map scripts at the same time. Of course, doing that would break plenty of existing mods (like mine) and nearly any custom map script, so I hope they don't do that any time soon.