Well, Sage Mode results from blending natural energy with the user's chakra to empower themselves. There are two versions of Sage Mode:
Imperfect Sage Mode occurs when someone improperly balances their chakra with natural energy, resulting in an incomplete, animalistic transformation.
Perfect Sage Mode is the complete version and doesn't change the user's appearance except for the pigmentation around the eye and the eye itself, such as the pupil turning into slits in Perfect Snake Sage Mode.
When Senjutsu is used with Perfect Sage Mode, it can interact with Yin-Yang Release and spiritual/intangible techniques when it normally wouldn't.