Earlier today when I was testing the effect of load order upon the modules, an unexpected result occurred.
Test 1.
I had my Journey of the Lone Wolf mod active first, and the Paint The World Red mod active second (this one gives an uber lava spell at the beginning of the game).
When I started a new game, there was only 1 character available in character creation, and that character received the bonus points upon reaching Cyseal beach. He didn't receive the lava spell however, which is consistent with only the Lone Wolf mod working.
Test 2.
This time the Paint the World Red mod was listed first, with Lone Wolf second.
When I started a new game, only 1 character was available at character creation, and that character received both the bonus points and the uber lava spell upon reaching Cyseal beach. *Both* modules were working.
Now the key difference between the two modules is that Lone Wolf makes its changes entirely within the Data/Mods/ folder, while the PaintTheWorldRed mod makes its changes entirely within the Data/Public/ folder.
The discrepancy between the two tests indicates that all of the Data/Mods/ changes are taking effect, while the game only reads the first Data/Public/ in the module load order.
