referrals from partners work better when related to the same office, but can work as well for different offices. I got a referral for my application at BCG Italy from a partner in the US, and was called a few days after that. In your case however it seems the partner already referred you or is willing to refer you to the Boston office – unless you ask them to refer as well for HK would be challenging to get the same strength as for the Boston application. You may ask the Boston HR to move the recruiting process to HK after interview confirmation, but you have no guarantee when and if they will be able to do so.
Since your concern related to Boston is on the visa, I would first clarify with HR if there is any issue with them sponsoring the Visa. If they are fine with the sponsorship, you can apply for the Boston office. If they are not fine with that, you can ask the partner if he/she can refer you for HK given the visa issue.
Hope this helps,