Ran the tests again with some more files, this time decompressing the pdf in advance. I picked some widely available PDFs to make the experiment reproducable.
For learnopengl.pdf I also tested the decompression performance, since it is such a large file, and got the following (less surprising) results using 'perf stat -r 5':
The conclusion seems to be consistent with what brotli's authors have said: brotli achieves slightly better compression, at the cost of a little over half the decompression speed.