This is some code that I picked up which I tried to implement. Its purpose is to create a form layer which is transparent, full screen, borderless, clickthrough, and always
Change your extended window style to only WS_EX_LAYERED, window style to only WS_POPUP (NO WS_SIZEBOX) and make sure to use DwmExtendFrameIntoClientArea with all -1's and this will produce transparent windows with layered support: downside is you need to bltbit with GDI from an offscreen directx rendering. Not optimal but it works. This gives mouse click throughs + directx rendering + transparency. Downside is you'll need to inform GDI anytime, pull the directx buffer (all of it or just the damaged portions) and write them to the screem with bltbit.
Setting the extended window style to WS_EX_COMPOSITED and DwmExtendedFrameIntoClientArea with all -1's (similar as above, WS_POPUP on the regular window style). This you can run directx from but no mouse clickthroughs. You can at this point define irregular paths for the hit mask and pass it to windows, its not perfect but if you know a general (non regular) area that can pass-through it'll work.
Still trying to find a true way of using opengl/directx on mac or windows platforms that can pass through mouse clicks with out having to do a bitblt to a legacy rendering system.