Yes, they have to be learned, which of course you can't do without the original remote. It is normal that not all commands work for all components, since there are so many different combinations it would be impossible to preprogram everything.
You might try one of the OneForAll remotes available at Walmart, preferably a higher model number, to see if it would give you these missing commands, or a way to access them.
If you get the 6820, 8820, or 10820, you could also use advanced codes.
Click
here to learn about advanced/discrete codes and which RS/OFA remote to use.