I can demonstrate this best in a PB, but I have seen these wrong Greek fonts in the middle of Logos edition books as well, just can't remember where at the moment.
Here's a document I created to demonstrate the use of all the fonts in my system capable of rendering Greek letters. In each case, the Greek word in the middle of this line of text is formatted in Word with Language = Greek and with the font named to the right (the rest of the line -- English -- is all in Times New Roman)

Now here is how that document compiles into a Logos PB:

Notice that in the first line, where the Greek word was in Times New Roman in Word, it appears to be rendered in a larger point size of Arial Unicode MS in Logos.
This is a pain, because I want the Greek lettering to look like it matches the surrounding text, which the Greek letters in the Times New Roman font too. And I don't want to have to go and find every occurrence of a Greek word in my PB (long document) and set it to some other font that will look better in Logos. Arial Unicode MS looks big and chunky compared to the same sized Times New Roman letters for English words.