I assume that by [siteroot]\..\packages
You mean that [siteroot] is the top most directory ? (top most of the enlistment)
And that the "packages" directory you mention is created under "Topmost \ Src \ packages".
If so, this is so that nugget is able to update the solution file correctly – so that integration with VS nugget, etc works with the default setup.
This directory is only necessary for that. If the solution is not found, the directory is not created and the package is installed directly from the stream.
This makes me believe that when you mention “folder is created in such a place that I can’t
access by using FTP” what is really happening is that the file is not being created at all as it is "by design".
"This seems to be also causing problems when reinstalling modules as it cannot delete the old module nupkg-file."
Could you clarify what "problems" are you refering to ?