Disclaimer: I have not actually ticketed a RTW trip with JL. However, I have looked into it (as a JL elite with Diamond status).

• JL charges a fee (per this old post it was 5500 JPY) to book a new ticket or make changes, including date changes that don't normally trigger add'l cost. 5500 JPY is not terrible but it can add up if you are constantly making changes to your ticket.
• JL phone wait times can be lengthy, especially if you don't have JL elite status. Even as a Diamond, the longest I've had to wait was probably 10-20 minutes..
• JL phone agents will generally refuse to even price out a RTW ticket unless the first segment is on JL. They will instead point you to the online tool.
• As with most non-US airlines, JL agents are probably hesitant to take on a complex request like RTW pricing in a language other than Japanese. If you don't speak Japanese, I expect you would encounter a lot of passive resistance on the phone.