The effect employed here require it to be a polygon, you can't do the same with a line.

One way to handle this is to just let the poly extend beyond the border of the map. The part sticking out will be hidden by the map border and the screen. The end result should be that it looks like a line.

The only difference between regular image exporting and rectangular section is that after you have clicked save in the save as dialog, instead of starting the export immediately, you will be prompted (on the CC3+ command line) to pick two opposite corners of your export (by clicking your mouse in the drawing or typing in the coordinates, either works). CC3+ will then export only the parts that is within the area defined by those points instead of the entire map.

The export process is explained in detail with images in the user manual, starting on page 47.

If you are printing, there is a tiling option right in the print dialog, just set the desired scale (battle maps for miniatures are usually 1' = 5" (as long as your map is mapped to scale in the first place)) and set the horizontal and vertical number of tiles. Check page 47 of the user manual for details.

If you are exporting it to image files first, you can use the "Rectangular section" file type exports. This will cause CC3+ to ask you for coordinates after hitting save, and this way you can save just a piece of your map. Just use this to export your map one piece at a time.

The file is locked for editing to ensure people don't create and publish modified versions of the document. Unfortunately, that also prevents creating personal bookmarks.

There shouldn't be any problem duplicating the file. All the pdf viewers I load the protected file up in allows me to use save as to save a copy, or I can just go into the directory (@documentation) and make a copy manually using the windows file explorer. But none of this will change the write protection of the file however, it will just give you a second protected copy.

To avoid scrolling to the page, I recommend using the bookmarks already there. Every single heading in the book is already bookmarked in the bookmark bar in the pdf file, displayed to the left in most pdf viewers. The entries are collapsed by default to avoid having to scroll through tons of bookmarks, it is easier to just expand the node you need. You can also click on the entries on the Table of Content pages to go directly to the page. If you know the page number you want, most pdf viewers also lets you easily jump directly to the page, in Acrobat for example, the shortcut is Shift+Ctrl+N, or simply click into the page box in the navigation bar and type in the page number there

I would say that's completely optional. According to Scott's description, those are "deep underground". They're also continent-scale, so his map isn't at a detail level that would show any potential dungeon levels, so if you want a connection, it could be as simple as putting a trapdoor/hidden stair in any room and saying it leads to a long tunnel going down to the Darklands, or as you mention, just describing one of your chasms as being really deep....