When I unload windows blinds, the canvas background in HelpNDoc is white.
So you are telling me that even though you can tell it to not skin a application, it will still skin some of it because like it or not the base colours (of the skin) have replaced the defaults? Yet, we can tell it to use a certain skin and the choice is there for no skin.
It is frustrating that I have to keep unloading WindowsBlinds when it gets in the way of certain applications and then I have to load it backup again.
That is how things work in Windows. You have a colour scheme but it applies to everything. Applications do not get their own colour schemes. If you have an application which does not look good with some colour schemes then often it is a case of the application using part of the OS colour scheme (say for the background) and then putting hardcoded black text on it. Basically they assumed backgrounds would be white in which case why did they ask for the colour scheme?
Excluding an application will exclude it from the theme elements, but not colour scheme as that is a system wide thing.
I would never recommend using a dark theme as you are much more likely to run into these issues with colour scheme assumptions.