If you disable the Auto Skill System, then you do get the Custom option.
This was the simplest solution to that not-working feature as it is quite a complicated one.
You should install the update first and edit InternalSettings.h later. Otherwise your settings will be overwritten once you install.
Work-around for that: Make a copy of your InternalSettings.h before installing, then you can put your preferred settings back afterwards.
its my normal fresh game install routine ive actually started nameing my PoTC game folders by date so i can tell which one is which as i have quite a few now , so the last Internallsettings.h is compatible with this release ? would have saved me 10 mins but its all done now.
edit: keeping in mind that i have 5TB of free space at the moment and i allso make a backup of the game folder once i know its working so if it screws up i can put it back to normal.