Ferdinand thought it was about the height difference.
Sometimes, it was indeed the height. But mostly, it was simply because society was used to ladies wearing heels.
It was the norm for ladies to wear heels especially on important occasions so Arabella as the Empress always had to wear one.
Only when she was just in her room at night could she wear comfortable shoes or slip ins. But if it was morning she would still wear shoes especially in her outer chambers where she receives visitors.
Her inner chambers were her only comfort where she could wear anything she pleases.
Arabella does love wearing them though since it fits her clothes. All her dresses were long so she had to wear heels to ensure she would not be stepping on her clothes or have to lift them all the time.
Likewise, she's already used to them. However, her feet still hurt from them, especially from the ones that were heavy since she had to carry their weight.