I noticed something in these lists that involves the way that these names are spelled in Egyptian characters. It has me wondering about whether people are transcribing things quite right. Based on the common transliterations I see, it would appear that all people see in these lists is alphabetic writing of the foreign names. I personally see in this a mixture of alphabetic and rebus writing.
Notice #3 (Kydonia), #8 (Kythera) and #10 (Knossos)? The three all begin with the symbol of upraised arms followed by a single stroke. Normally this is the way of writing kȝ 'soul', often written out "the Budge way" as ka to avoid the pesky issues concerning vocalism in a script that normally didn't write vowels (except in foreign names like the above, of course). The actual pronunciation in Middle Egyptian was likely *kuʔ. It just so happens that a syllabic reading of this symbol as ku suffices excellently when sounding out the names Kydonia and Kythera. Knossos can also be read this way if we keep in mind that the stress is placed on the second syllable. What I find interesting is not only that we can get away with reading this out syllabically based on a literal reading, but also that this symbol of all things was chosen, a symbol clearly of religious importance. It'll relate to what I write below in a minute.
Also look at #8 (Kythera) again. We see a mouth symbol followed by another one of those strokes. In everyday writing, this would write the literal word for "mouth" and was probably pronounced *rāʔa or *rāʔ by this time (> Coptic ro). Just as before, a syllabic pronunciation based on the literal reading, ra, gives us precisely the vocalism we need in the name Kythera. Interesting, no?
Now back to the religious symbolism in the first set of examples, it continues on in #2 where we see another spiritual glyph starting off what is thought to either spell out Phaistos or Pisaia, a bird which normally represents a second aspect of our tripartite being, the ba (according to Budge spelling, at least). Again, the actual pronunciation was slightly different, probably *baʔ, but in this case Budge's spelling is close enough to reality. If we can get away with syllabically reading ku and ra, why not also ba here? If so, the alternative reading suggested, Pisaia, is not possible. Yet while this works in favor of the reading Phaistos, this interpretation also remains problematic if going by the Mycenaean name *Phaistós (PA-I-TO).