Both questions are correct, but they have slightly different meanings and uses:
1. "How is it different from Tom's?"
Meaning: You’re asking about the specific ways or aspects in which the routines differ.
Naturalness: This is the most common and general way to ask for details about differences.
Example:
"How is it different from Tom's?"
"Well, I wake up earlier, and he exercises in the evening while I don't."
2. "How different is it from Tom's?"
Meaning: You’re asking about the degree or extent of the difference. Are they slightly different or completely different?
Naturalness: This sounds more precise, especially if you want to know how much the routines differ.
Example:
"How different is it from Tom's?"
"Very different! My routine is completely opposite to his."
Summary:
Use ① (How is it different...) when asking about specific details of the differences.
Use ② (How different is it...) when asking about the degree of difference.
Both are natural, but the first one is more common in everyday conversation. 😊