I thought %% was some sort of macro expansions and that is how magrittr creates pipes. But browsing through the magrittr github repo, it looks like they just define %>% and the other pipes as functions [1].
I don't actually know the relation between magrittr and the RStudio shortcut, but I've always assumed a shortcut for typing the pipe characters exist because RStudio employs Hadley Wichkham, who in turn is really big on tidyverse and pipes.
Would %>% mean anything in R if you didn't import magrittr?
[1] https://github.com/tidyverse/magrittr/blob/8b3d510f2a333b224...