One option for doing this is to export the pipe from within the package itself. This may be done in the 'traditional' zzz.R or utils.R files that many packages utilise for useful little functions that are not exported as part of the package. For example, putting:

#' Pipe operator
#'
#' @name %>%
#' @rdname pipe
#' @keywords internal
#' @export
#' @importFrom magrittr %>%
#' @usage lhs \%>\% rhs
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