(a) The user will be lost quickly where to navigate next. To use more than 3 levels is only beneficial if it closely matches a hierarchie already made up with those levels (e.g. FTP view). For that however it is better to list in the "sitemap" simply a "directory" to navigate into and use its own sitefile for the subdirectory. Make it known with a slight variation that the user has gone to different space - away from frontend web presentation into a hierarchic download section. Same applies to moving over to a forum / webchat space.
(b) How do you think you can place all the levels in a single navigation bar. The recommended way of mksite.sh is to use horizontal rulers for each "sect1", to use an itemized line for "sect2" and place below the item more "sect3" nodes possibly many per line. That's compact enough so the user does not get lost in the middle. Note that mksite.sh does not encourage folder-expand/folder-close menu-handling but instead strongly hints to use a sitefile not changing on every click thereby making the "next-page" to jump away and up and down. Otherwise one would need an explicit "next" button somewhere to help with sequential reading and searching (the usual "browsing" action takes 3 seconds per page on average).
The human mind can only catch about 7 items at a time with one look. Going beyond that confuses the human brain and slows down information gathering (stress). On the other hand it is usually not interesting to use less than 3 items per section, it would get overlooked quickly among other sections. Therefore (a) add topic pages to section as they fit (b) when a section overflows with 8-10 items then split the section in two with each 3-6 topic items.
When a topic gets too long it is not a good idea to keep everything on a single long page that the user has to scroll down - searching for some interesting subitem. Instead cut the long page into pieces and register as its own html page with the sitefile. They all shold be on the same topic anyway so let's register the page on the sitefile with a very short hint only, possibly just use numbers. And if not using number then use common shorthands such as "intro" "related" "main" "links" written in <small> letters on the sitefile navigation bar.
If there are too many splitpages then make the first of its series (the subsection topic item on level2) a frontpage with a href to each splitpage and short description of the content of that splitpage
The three levels make enough room for pages - a big website for mksite.sh would be using 6 sections with an average of 6 topic per section and an average of 3 pages per topic. That makes more than 100 pages. If a section gets too long one can also make for multi-column layout (with some global quicklinks) but do not be tempted to put too much into such a column.
Instead consider to split the website into multiple spaces with each its own sitefile. That can be to put them into directories of the main website (developer, user, etc) and make a seperate sitefile for the main website that goes to introduce the purpose of each area and linking into each area then. The site map will only contain a single entry per area and otherwise lists the items of the intro website.