It can be closed with status Won't Fix. These lines of code ConfigSheet explain why, after removing plugins/buttons - it loads all toolbar (default).

That's why it's recommended to define toolbar (which again requires some time due to manually typing) instead of removing items manually.
How to remove buttons from CKeditor 4 - Stack Overflow

how to show ckeditor with basic toolbar - Stack Overflow

Anyway, there are plenty enough examples and even FAQ entry