As you mentioned, there are 3 points:

1) When to generate the web pages ?
In my opinion, the 'player guide' is used by 'standard players', who are using
the current game release.
So the 'player guide' must be in sync with the current game release.
Consequently, it has to be generated during the 'release process' (either
automatically by a slave-worker or manually, it does not really care at this
point of the discussion).

2) Where to put the generator ?
Well, as it was said, the generator's input is in freedroid-src, but its output
has to eventually go in freedroid-website... There is a strong interdependence :
the generator has to be adapted after a change in the data source
(freedroid-src), but it also has to be adapted in case of a change in the
website structure (freedroid-website). So, one repo is not better than the other.
In such a case, the usual solution is to used an 'exchange file' in an 'exchange
format' which is 'agnostic' of the data structure "in" the game and the data
structure "in" the website.
Then, the generator should perhaps be split in two parts: one part in
freedroid-src, which writes out the exchange file, and one in the
freedroid-website, which reads it.

3) Which language ?
Well, I would be in favor of using a 'standard' interpreted language,
specifically if (a part of) the generator is in freedroid-website (there is no
compilation process during the website generation).
And, in my opinion, given the computations needed, python is indeed a better
choice. However, the 'clean' process would be to write a docpad plugin...

[just some thoughts...]