Hmm... Looks like a test is in order. I would like to know for sure how TA works. I do know that in the past, each upgrade raised the total by 5%, as I count how many are left by that number. It is always x4 then x9 (as in plus 5) and then x4 and then x9.
Except that the first upgrade is 4%. The initial value is 5%.
For TA, they remain the same, with the exception, as you mentioned, of not all races getting all modules; as well as the fact that the Drengin get a 10% and an 8% respectively in their tree to make up for not having access to anything beyond the first two modules (the 4 and a 5). With the initial 5%, this places their maximum at 32%, as opposed to the 39% one could reach in DA (and possibly DL...it's been a while). Compared to some of the other Twilightians, this isn't half bad-but that's neither here nor there.
On the system I'm currently on, the game takes ages to load, so screenshots (for instance) are out of the question, but I've verified these numbers sufficiently with the use of Galactopedia.
Ragnar1's recollection, albeit incorrectly, of another module providing a 4% mining bonus is no doubt due to the production modules on economy starbases having a significant number of 4% modules (incidentally, they also finish it out with a 3% module). I was also under the mistaken impression that the mining starbases had more than one 4% upgrade, until I checked.