It all depends on what you call “intuition”. Usually, this means “my routine and I didn’t read the manual for the new application”.
In numbered list configuration (and chapter numbering is just an avatar of a numbered list), Aligned at defines a reference position for the number. Number will be positioned at Left, Center or Right of this position. What is upsetting is the fact that if you choose Left (default) the number will be flushed “right” against the reference position.
Consider that the Aligned at distance defines a “first line indent” for the number while the real paragraph left limit is still based on the declared Indent at (which takes precedence over the [discarded] value in the paragraph style) upon which the final paragraph alignement, left/center/right/justify, is based.
Therefore, an incorrect choice of number alignment results in a visually incorrect center layout. For center, always keep Left. Be very careful with Aligned at (~ first line indent), Indent at and Tab stop at. They interact on the final rendering. Unless you have very specific needs, keep Aligned at at zero. Play with Indent at only if you expect your heading to be multi-line and set Tab stop at the same value. But multiline-heading is barely compatible with centered heading with number on separate line. In this latter case, keep defaults, have the number followed by newline and let Writer do the job nicely.
That’s very clear, I had no idea there was such fine tuning!