Yes. There are two main ways to open a document. One is without specifying any options other than visibility. The other option is to specify some options. If you do not specify any options when opening a document by code, then the application options settings will be used. If you specify options, then it will obey those specified options.
Below are links to the online help documentation for those two methods that are usually involved.
Documents.Open
Documents.OpenWithOptions
Example of opening an assembly with options specified:
Dim oDoc As Inventor.Document
Dim sFDN As String = "C:\Temp\MyAssembly.iam"
Dim oOptions As Inventor.NameValueMap = ThisApplication.TransientObjects.CreateNameValueMap()
oOptions.Value("SkipAllUnresolvedFiles") = True
oOptions.Value("DesignViewRepresentation") = "Default" 'name of DVR (view rep)
oOptions.Value("ExpressModeBehavior") = "OpenDefault"
oDoc = ThisApplication.Documents.OpenWithOptions(sFDN, oOptions, True)
'do something with that 'oDoc' variable now
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Edit: There is also a way to determine which DVR (DesignViewRepresentation) was the last one active in a specified file, using the FileManager.GetLastActiveDesignViewRepresentation method, which returns a String representing the name of that DVR. Then that could be used when specifying the name of the one you want to be active when specifying options, and which DVR you want active when you open it. That FileManager object is obtained directly from the application object ('ThisApplication' term in code) (Application.FileManager).
Wesley Crihfield

(Not an Autodesk Employee)