Thanks for the great tip Dave!
Draken 5.1 will be compatible with both Prepar3D v4 and v5, so you will actually be able to install it in a single location. The dynamic lighting fx have been modified to work in both versions, so there will not be any P3D v5 specific content in Draken 5.1.
I work in a single folder structure during development and put symbolic links to that in the Prepar3D v4 Add-ons and Prepar3D v5 Add-ons folders. But for a normal user it is more convenient (and easier) to edit the add-ons.cfg file.