At the time I was testing 10.4 and then 10.4.1, ESRI had confirmed this was a bug and that there was no fix or workaround yet. I was forced to migrate backward to 10.3.1 because of the following bugs which had no fixes
1) This one - pdf exports only partially both in Desktop and in Scripts (still no fix at the time I write this)
2) Services which took 10-15 seconds to publish in 10.2-10.3 took 15-20 minutes on 10.4.1 resulting in that much service downtime. (per my other thread, ESRI later released a bug fix for this)
3) Bing maps do not work in PDF exports with ArcPy on ArcGIS server (does work on desktop). This one was broken in previous versions as well, just not fixed yet.
4) Not compatible with SQL Server 2008 R2 (This one is not a bug. ESRI does not claim it is supposed to work. Do not try it even temporarily. It caused corruption when testing to see if we could temporarily get by)