I've been using rollupify in my projects for a few months now with no issues, but I didnt know it didnt work on npm modules. I would be interesting to see benchmarks of rollupify vs rollup on ots own to see if its worth changing bundlers.
Overall though there are still lots of edge cases that aren't well-covered without plugins (such as globals like process.nextTick etc.). Some details here: https://github.com/rollup/rollup/issues/552