I think I narrowed the problem: this only happens when choosing "printer" output in the Color tab of the PDF export window. Could it be a problem related to color profiles? I'm not really familiar with all that, not sure what could be the cause, but I guess this should help to understand the nature of the problem.
[edit] and also, it happens when exporting with compatibility for PDF 1.4 or 1.5. Looks like there is no problem for PDF 1.3.
Do you think that even with this rendering issue on the screen, there is a chance that fonts will be correctly printed? (Well, I don't have a printer here I cannot try.)
(Also, I updated both Scibus and mupdf, doesn't help.)