I think it's a very nice gesture. I think I read somewhere that a red flag in therapy is when you have to keep paying for multiple extra sessions to fix what happened before.

I dont mean ruptures just if it is an ongoing pattern where he says something semi unkind that causes you to panic and then spend your money to "fix" what your t did. This seems more like he accidentally triggered something and was willing to work to fix it rather than lose you as a client.

I think as a one off it could be acceptable. I insist on paying t every time we have a call. One week she said as the call had been short (2 or 3 mins) and was a question about something that happened in t, she viewed it as an extn and there was no charge
I thought that was a thoughtful thing to do and she has clearly put some thought into what she felt was appropriate. So hear him out and see what you feel comfortable with.