With the pdf open in Acrobat go to Advanced > Preflight > Standards > PDF/X-1a:2001 (check Apply Corrections) and save. After the file is created, you could right click and choose "Convert to AdobePDF".
Once you have your colors worked out and just to add another pdf option into the mix: you could use Scribus' export to an eps file. I did change the default resolutions from screen to printer quality. The on-screen quality did not appear to be top quality, though I have a lot to learn about the available Scribus settings. I do not have a printer here now to test how my example document pdf actually looks when printed on paper. There could be significant differences in color appearance when printed on coated versus matte stock, etc.
Another color consideration would be the type of paper you will be using. RGB is a color model for electronic devices, not for printers ()-what you see on your screen may or may not be close to what you would see on paper. Scribus has a wiki page on spot colors () and has a page that may also be helpful ().
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.
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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.