I think you’re doing things backwards.
Again, the score you get doing “File–>Print–>Save as pdf” is perfect.
In my opinion You should not change your settings in Score Editor to get better results for display on computer only, because as you know it will be differently displayed depending on the viewer used.
Besides, I don’t know what is the final goal of your score, but doing so, you would get unwanted results when you’d want to print it.
The only viewer that should be considered as a reference is Adobe Acrobat.
That brings us back to the most important post of this thread:
Please view your score in Acrobat and make sure you change the settings in Acrobat as follows:
Edit>Preferences>Page Display then in Rendering section, uncheck “Enhance thin lines”.
For “Preview” on Mac, try to find if there is any similar setting.
If you still want to go for bitmap images in PDF, you should try this:
1- Export your entire score in PDF with “File–>Print–>Save as pdf” from Score Editor
2- In Preview export all pages to images (PNG)
3- in Preview convert all exported PNG back to PDF
Finally, regarding your icons display issue, I believe you should contact Apple
Hope this helps.