How do I repair my partially rotted subfloor?
Your plan to use your circular saw with the table set to depth is good. Even if you were to cut tight to the wall and tub, you still aren't getting all the damage, so a short distance out is fine. Personally I'm not a fan of joints right at walls and tubs anyway. I'd rather have an offset.

When you do the repair, float lumber under the remaining damage, with construction adhesive between, wherever possible to support it. 

The fact that the damage extends under the wall probably isn't a serious concern if you haven't seen any significant side effects, such as settling or floor damage in the adjacent room. I'd be fixing whatever you can reasonably access and calling it good. It'll be a far cry better than what you have now.

FYI, a "toe kick saw" is actually called an "undercut saw".