OK, so to add to what I wrote (perhaps someone may find it useful): indeed the culprit is the macOS Universal Conrol -- disabling it has the desired effect of PDF being embeded, and I can choose which PDF passthrough mode to use. Now interestingly, what see is that: if I select "Passthrough" then ligatures, etc. are preserved as in the original PDF, however the color is still not CMYK (my AD document is set to CMYK/8 and I use CMYK sliders and the color picker to check the CMYK values of the font). If I select "Interpret", then I am getting correct CMYK value for the font, BUT, ligatures get enabled and there seems to be no way to disable them. Moreover, the "Interpret" seems to be ignoring whatever defaults I saved for the "Typography" tab (I am ceating new document, then I am setting Typography options and finally I go "Edit->Defaults->Save".
In summary, I can either have disabled ligatures or properfy set the text color but not both 😞
Again, any help will be much appreciated...