Actually, you are right!
I created smaller buttons inside GUI-builder and it looked smooth in my window. When I created larger buttons, I started to see the non-smooth texture again.
So, yes, GUI-Builder is nothing different than creating the buttons manually in terms of texture smoothness.
As a reference, the buttons size used in the screenshots I attached were 256x64 on a window 800x600
I created smaller buttons inside GUI-builder and it looked smooth in my window. When I created larger buttons, I started to see the non-smooth texture again.
So, yes, GUI-Builder is nothing different than creating the buttons manually in terms of texture smoothness.
As a reference, the buttons size used in the screenshots I attached were 256x64 on a window 800x600