After realizing the Color Management click and thus having PDF-x-1a appear as an option to export, I selected File > Export for my book cover, sailed through Preflight Verifier without a peep, selected PDF-x-1a, hit the Save button and off it went to my desktop. Doing a random check, the results of the PDF-x-1a export were pretty shocking. My images were fine. The spot colors were distorted somewhat, but not bad, smoother even; however my text font had been changed from my embedded Baskerville to a sort of Arial. Trying PDF-x-3 produced the same result.
Prior to viewing this I was reminded that the export should be opened with a PDF viewer, in other words Adobe Reader (red logo). I discovered my Adobe Reader had disappeared and been replaced with Acrobat Reader DC (black logo).
This may be important because I wonder if this is a Scribus issue at all.
As an experiment I went back into File > Export selecting instead PDF-1.3 first, then the latest PDF-1.5 (Adobe 6), and then from EPS converted to PDF. All three of these PDF's saved the book cover fine in every respect when viewed using the, now, Acrobat Reader DC.
All five of these exported PDF's also had in common a pop-up message: "Cannot extract the embedded font 'Baskerville'. Some characters may not display or print correctly." with an OK button (see screen shot) Clicking-off the OK button produced no change in any of them.
Has anyone who is still fortunate to have the old Adobe Reader(red logo) experienced problems with Scribus PDF-x-1a exports?
( I answered my own question; Transferring my Scribus book cover to an different Mac that still hadn't lost its Adobe Reader 10 (red logo) and exporting it as a PDF-x-1a, voila, a perfect book cover, Baskerville and all. I gather I now have finally a perfect book cover saved in the holy grail PDF-x-1a.)
From this experience the modest advise might be, if you have Adobe Reader (red logo) hold onto it for dear life and steer clear of solicitations to "upgrade" to anything now named Acrobat Reader DC (black logo). Downloading the black logo appears to wipe out your red logo and as a modest suggestion you should be very wary of the latter. Maybe the two can exist together but to chance it you won't be upgrading your old read logo; there is none.
Even though my journey may have ended with this discovery (cross your fingers), it might be helpful to others to still continue.
Since the PDF-x-1a is a requirement set by the behemoth Ingram Spark and its subsidiary, I have taken this issue up with them concerning only the black logo PDFx's mashing up and what if anything they intend to do about it. It seems to me they should vet these themselves before subjecting their clients to a merry-go-round of submissions as has experienced by some of their DIY publishing clients. Ingram Spark responded that it would be passed on to the "Premedia Team for their "insight".
In case it might be helpful, I noted that all five of the PDF Exports mentioned herein opened in Acrobat Reader DC, but with differences in their windows. The three that show the book cover just fine opened in windows with the tool bar extending across the top row. The two that were either of the two PDFx's opened with tool bars that also extended down the left hand side as well with one icon being called Standards with the immutable information that went with it (see screen shot).
I queried these PDFx windows further using their own File > Properties and found they first recognized that my book cover had been generated using Scribus 1.4.6 and the PDF producer was Scribus PDF Library 1.4.6, but black logo had shown it as PDF-1.3. The garbled font was recognized as Baskerville, TrueType, but "encoded" it as "Custom" and "Actually" installed instead something called "Adobe sans MM Type 1" (must be a sort of Arial). I proceeded to Custom and found nothing that made any sense to me, but based on reviewing other posts may mean something to those with more expertise: Name: GTS_PDFXConformance Value PDF/X-1a:2001 Name GTS_PDFXVersion Value PDF/s-1:2001. The only thing I took away from this is that the black logo knew damn well these messes were PDF-x-1a or PDF-x-3.
I hope this helps.