For leaves the simplest way is to create your leaves in a particle system on an object in a separate .blend file and link or append this particle system to the file that contains your tree. After this the new particle system should be available in the particle settings drop down in the particles tab of the leaves object (this is an object parent to the tree skeleton and separate from the trunk object as well). When you click Update tree the appropriate number of leaves will be set.

Any material can be applied to the mesh that represents the bark. The mesh is uv-unwrapped, see technical details section on which uv-maps and vertex color layers are available.

Interactively drawing lots of branches and leaves requires a decent video card. Performance tends to be less dependent on the CPU. NewGrowth should work with any video card that is supported by Blender but to get a decent performance a GTX 970 or better is recommended.

No. Although it shares the same algorithm to generate the branches the resulting tree object is different.

You might have enabled emulate 3 button mouse in File → User preferences → Input. This causes left alt + left mouse to be interpreted as a middle mouse button action. Either disable this option or you might try the right alt button (although that might not work on all keyboard layouts / operating systems)

Interactively drawing a tree in the 3D view is designed to make use of the lighting you set in solid mode with studio lights. In any other mode (Eevee, Cycles, Matcap) these lights are not available. If they are not available they are replaced by a fixed set of studio lights that may not correspond to the rest of the 3d view (and in older versions there was simply no light and therefore black leaves).

Once you have finalized your tree you can change the emitter mesh and the other objects as well but these will be regenerated once you click the Update Tree button so it would be wise to duplicate those meshes first.

No, or more accurately, most of it not. It is ok to move vertices around but you shouldn’t delete any of those vertices because they also contain other information that is needed to generate the other meshes. Removing a vertex will result in errors once you click the Update Tree button and you will not be able to generate the trunk or leaf emitter again.