There are many things you'll find on at NI's website, which makes me think that at least some people there must be banging their heads running into these issues, so maybe there is hope.
There's many ways to skin this one: I take the RTE distributed by NI, run the self-extracting EXE locally, then package up the result into my installer. At run-time I evaluate which (32 or 64 bit) to extract/execute and call the setup.exe with "/q /AcceptLicenses yes /r /disableNotificationCheck" (reference).
I'll add my code for checking if the native version of the LV RTE is present:
function IsLabVIEWMissing: Boolean;begin result := not RegKeyExists(HKLM, 'SOFTWARENational InstrumentsLabVIEW Run-Time13.0');end;
Tests like this are evaluated in the Files and Run sections to determine if the appropriate item needs to be executed. Similar tests for .NET, MSVC.