I also experienced the same while makeing DNN 5x PA for our modules. I discovered the same solution as Kelly Found has mentioned. However, I did not want to move the dll and resource files into bin and localresources folder insize the zip. After some more research I found Charles Nurse's post on manifest's file component. It says that  you can also use <sourceFileName> element if the Source file path and destination file path are different. Since the Assembly component inherits file, I tried the same <sourceFileName> in my assembly component. Works smoothly. Now,  my DLL files can stay in the root folder  of the zip file. 

Hope this helps someone else also.

Prabhash