Just to address one of the original questions briefly, regarding the "cluttered" looking main window, one of the strengths of BibleWorks (which may or may not also exist in Logos, I don't know) is the ability to view text in a variety of different ways.
If you just want to look at a stretch of Greek or Hebrew text, say, without search and analysis windows, you can open a new browse window, which will "float" above the original BW window, and read in it, mark it up, etc.
If you want to look at the Hebrew and LXX of a particular passage side by side, with no other complications, you can open a parallel versions window with just those two versions (or any other versions you want), again separate from the main BibleWorks window.
If you want to look at parallel biblical passages side by side, from the gospels, say, or from Kings and Chronicles, there are predefined synopsis views, or you can create one of your own fairly easily. Again, this is in a window separate from the main window.
So you can pretty well customize your viewing and study of the text to your needs and preferences. You can have multiple instances of these types of windows open, and parallel and synopsis window setups can be saved to use again later.
You also mentioned at one point studying the use of the Jewish scriptures in the NT. BW comes with Gleason Archer and Gregory Chirichigno's Old Testament Quotations in the New Testament, which is fairly useful for this. It also comes with the NET Bible notes, which include cross-references to Hebrew Bible quotations; hovering the mouse over the reference will pop up a window with the text, and you can configure what versions appear in the popup.
So, from a user-interface perspective, there is just a lot of configurability in BibleWorks. I have no idea how that compares to Logos, not having used the latter, but I think it's a real strength of BW.