All of my needs except for certain runs of business cards would best be served with process colors instead of spot colors. It seems like there is some confusion regarding spot and process colors. When creating a pdf, hover your cursor over the option and a description will pop up that may be helpful. For the 'rely on system fonts' setting, you would almost always leave it checked. The answer may be painfully obvious to Scribus pros out there, but I am stumped unless the font's license prevents embedding. As you suggested, the resulting pdf page became an image instead of a combination of image and text and there does not seem to be a way to override this behavior (at least for the fonts I tested). I downloaded and tested Scribus today and found that my fonts were being converted to outlines in Scribus instead of being preserved as embedded fonts. My experience primarily involves other Adobe products like InDesign and Illustrator and Microsoft products like the Office suite, Visio and CorelDraw. I should have taken a look at Scribus before responding-Scribus does not interact with Acrobat like other programs I use do.

Adobe acrobat pro 9 pdf/x-1a settings