I must be missing something, as I cannot be the only one who has noticed this, given that Autoloader has been out since AutoCAD 2012....
It is quite common for users to configure Support File Search Path (SFSP) at session start via Acad.lsp (as I've done for years), but doing this strips all .bundle-centric SupportPath XmlAttribute values loaded by one or more PackageContents.xml files located in any of the multiple ..\ApplicationPlugins\ folders which are implicitly trusted.
Autoloader (ARX, or .NET?) does the loading of an App-dependent SupportPathXmlAttribute values prior to any Acad* file in the startup sequence... Which is how a basic Acad.lsp file can overwrite these App-dependent support paths.
Are we (users) expected to account for this potentiality by now being responsible for parsing SFSP for any ..\ApplicationPlugins\ reference, in order to support any user-downloaded Exchange Apps, and/or internal Autoloader Apps?
Another option would be to invoke:
(command "appautoloader" "_reload")
... Once done configuring SFSP, but still, this shouldn't be required (I feel).
Why doesn't Autoloader already handle this in the code-behind?
Cheers