All biological systems exist as equilibria, so it's more than likely that there's a percentage that's ubiquinated as well as that which isn't.
And as far as I'm aware, diastase isn't a stain. Going off my head here from a UWorld practice question I had done some time ago, the periodic acid oxidizes C=C in glycopeptides (and fungal polysaccharides) to aldehydes, which react with fuschin-sulfurous acid to form a magenta color. Diastase is then added in order to dissolve the glycogen, meaning that it yields a negative reaction with PAS staining. The only reason T. whippelii appears magenta is because the glycopeptide is diastase-resistant.
Also, regarding CFTR, I'm not so sure that that's notably ubiquinated as you've stated. Almost any practice question I've come across has suggested that it's found sequestered as misfolded protein within the RER.
With respect to ubiquination, I do recall from UWorld that autosomal recessive Parkinson's disease with age of onset < 50 yrs can occur due to mutations in Parkin (and two other genes that I can't remember the names of right now), which result in a defective ubiquination complex.