Your first suggestion, adding the "Configure Tools" at the bottom of the menu, was not done for techincal reasons, although probably not the best technical reasons.  When that menu changes, it's far easier to leave the first two items intact on Windows than to move them to the bottom of the menu after adding items.  Again, it's not a particularly good excuse, but that is why things are the way they are.

I've thought about your suggested addition before, and I haven't come up with exactly the best way to do something like that.  I'll look into it more, though.

SUGGESTED CHANGE
Make 'Configure tools' and the horizontal break line appear at the bottom, not the top, of any list of tools the user may have added.

SUGGESTED ADDITION
Create an extra Help menu, a bit like the Toolbox menu.
It could site next to (just inboard of) the present Help menu.
Call it something like 'Manuals' More help', 'Help2' etc (of these, I prefer 'Manuals').
Provide a 'Configure manuals' facility, a bit like 'Configure tools'.
As before, have it appear always at the bottom of whatever drops down.
Enable users to select and save links to .PDF .txt  .docx,  .RTF  .htm .html (etc) files.
Either use (or default to) system default readers for each of these or put some paths to userpreferred readers in the 'Options' menu.

Users could then very easily and swiftly save and point to (in the config tool) copies of (eg) DISLIN, Gtk and LAPACK manuals, a Fortran-95 and Fortran 2002 manual, etc., which would then be instantly accessible whilst coding, from a single SF menu click.

We can already do this with the Toolbox menu, and I do - it is extremely useful - but it does take quite a bit of faffing about.  One has to find a suitable reader for each entry, sometimes experiment with the calling syntax and trailing options, then enter enter no one but two pathnames in each Toolbox entry every time - one for the saved manual and one for the appropriate reader.
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John