I'm not sure if this is a bug or intended. With this code:
mesh_0.setTransparency(255);
mesh_0.setTexture("tex_with_alpha");
mesh_1.setTexture("tex_solid");
Object3D mesh = Object3D.mergeObjects(mesh_0, mesh_1);
Then the mesh_0 part loses the alpha setting (100% transparency --> black).
Sorry if this has been discussed before.
(Tested on Sony Ericsson Xperia Play.)