Could you post screenshots here of how you view some of this data in ArcMap, ArcGIS Pro and Adobe Acrobat? Just hit the "Print Screen" button on your keyboad and paste in a graphics application if you want to crop the image, or straight in a GeoNet editor window, which also works.
One fundamental difference though between ArcMap and Pro, that also may affect how you "view" the PDFs, is that Pro currently maintains all coordinate information of the original data in the PDFs, while ArcMap does a kind of "generalization" to the dpi specified during export. This difference, as I understood it, has to do with some fundamental, Windows level, differences in the display pipeline of ArcMap and Pro. As to some observation by me regarding this, see this post I created in another GeoNet thread:
https://community.esri.com/thread/179579#comment-710329
As a consequence, if you have highly detailed data derived at large scales (e.g. 1:5k-1:25k), and view it a small scale (e.g. 1:100k-1:M) without generalizing the data yourself using a tool like "Simplify Line/Polygon", the data may appear very erratic and with "spikes" in a Pro export if the data is also following erratic paths, while ArcMap's output may look smoother and closer to what you would have expected. Especially look closely at the screenshots I posted there to understand what I mean and the differences this may cause in the visible image on your screen.
