Given that, as established earlier, the Arduino is programmed in C++ and that the transformation from a program using setup and loop to one using main is trivial, I think you're worrying too much. Any coding you do using the Arduino IDE is directly relevant to building your C++ experience - the functions you write would look the same whichever skeleton they use to get invoked. If you're going to be working with other platforms, you might want to get used to direct port access and bit twiddling, but even there, you can write your own wrapper functions (if they don't already exist) if they're fast enough.
In short, don't be so concerned about whether it's 'pure' C++ and get down to some coding instead 