A software appears non-intuitive when ine does not make the effort to read the documentation.
At minimum, the built-in help is a valuable source of information. It is not a tutorial, it is very concise as a reminder should be and one has to collect all the bits and pieces to build the big picture. But it is there in every decent installation.
A much more detailed and progressive source is the official user guide. One again, you must read a few pages (do you drive without lessons first?).
Now for the oversized window hiding important controls, the cause may be an incomplete dependency installation. LO has specific modules for GTK, KDE5, KF5 and perhaps others graphic elements. I don’t remember what’s Xfce basis, but it should work with GTK, at least after some initial uses of LO to adjust window sizes.
The TOC pop-up dialog has a combo box labelled Evaluate to level in Create Index or Table of Contents section. This allows one to limit the depth of TOC to the desired level. Though the default is 10 (all levels), you might have unintentionally changed the value to 3 during your fiddlings.
Creating a TOC is very simple when you’re satisfied with the defaults. Playing with the controls, you can design very complex and sophisticated layouts. I recommend you first learn with simple default TOCs before trying custom layouts so that you understand thoroughly the effects of each control.