There are no differences in the two installation "modes" as you call them. You install the same server software and the only difference is, how you obtain the server.id, names.nsf and admin4.nsf.
Lets take the Public Addressbook (names.nsf), as that one is the one responsible for your problem.
In a "standalone" installation the names.nsf is created from the template pubnames.ntf in the version of the install package (in your case Version 9.0.1).
In the "additional server" installation the names.nsf is replicated from the main server. In your case the main server is 8.5.x and that means that the version of the names.nsf is 8.5.x. If x is smaller than 3, then the template does not contain the settings, as this feature came with 8.5.3.
That means: You need to update the names.nsf with a current template. Please ask somebody with admin rights to do this for you. An 8.5 server works with a 9.0.1 template without any problems, so updating is not an issue.
But if the template contains customization then this has to be done in the new template as well.
In addition: Depending on the admin it is absolutely possible to have an 8.5.3 server with an 8.5.1 template.
The setting itself in addition is hidden, if the option "Load Internet configurations from Server\Internet Sites documents:" is "Enabled" on the Basics tab of the server document.