Logo configuration when generating apk in Unity 5

I do not know if I understood your question well. From what I understand your game is landscape but the splash screen is in portrait?

I would not know how to solve without looking at your code or configurations in unity, but as far as I know the unity logo respects the orientation seated in Edit > Project Settings > Player > Resolution and Presentation. If you have more than one selected it can default to protrait, but just for testing go play with the settings to understand better. Another thing you can do is to put a setting such as "Just portrait" and spin the rest of your game with the code:

Screen.orientation = ScreenOrientation.Portrait;

Just put it in any Start in your scripts.

If I'm not mistaken, the logo of unity with the cell phone (portrait) is just the same. If you are using unity pro you can change the image.

In the build configuration (player settings), you can choose the default orientation of the game (landscape, portrait, auto rotation, etc ...).

File - > Build Settings - > Player Settings - > Settings for iOS (or) Settings for Android - > Resolution and Presentation - > Default Orientation