Before you get ahead of yourselves guys this not one those sage mode gives affinities to all chakra elements thread. This is different and focuses on the training aspect of nature transformation of chakra regardless if you have an affinity to that element or not. Also this isn't only targeted towards Naruto in particular but since he uses sage mode and a lot of us suspect he may have a 2nd chakra element he is most applicable for this theory.
So what I'm theorizing here is.
Can sage mode HELP a user LEARN nature transformations? I believe it can and here is my theory on the matter.
Sage mode has shown the ability to visualize chakra within the users mind as shown with Naruto which he located Nagato during the Konoha attack. Also Naruto was able to distinguish between chakras such as Hinata and Kakashi during the same konoha attack. Here are the pages where Naruto is visualizing his own sage chakra and tracing it back to Nagato via the chakra disruption rods to Nagato.
Similarly when learning nature manipulation each chakra element has its own way the user needs to visualize his own chakra to carry out the training. For example Naruto asked Asuma for help regarding wind nature chakra, and Asuma said to visualize his chakra as two parts grinding against each other making each part sharper and sharper. This is where Asuma tells Naruto about the visualizations regarding wind nature chakra.
So can sage mode help a user visualize this for chakra elements? But how would it know you may ask? And the answer is the connection with Natural energy with all things in the environment. If Naruto entered sage mode where there are areas of lots of water or fire or wind or any of the elements the natural energy within these natural wonders may help Naruto understand how to undergo nature transformations with the help of understanding how natural energy interacts with the elements out in the environment.
I suspect it will be ma/pa/great toad frog will reveal this aspect of sage mode due to their vast experience with sage mode. Similar to kakashi who told Naruto of shadow clones other uses of learning something which he didn't try when using shadow clones all those years before hand.
NOTE: SENSORY NINJA ABILITIES VS SAGE MODE SENSING ABILITIES
Sensory ninja are different in my opinion and sage mode goes about things differently when it comes to sensing and wouldn't be able to what I'm saying in my theory.
There you have it, what you think?