I have NO IDEA how the "One-click-install" version of ISTA you have works. If it correctly interfaces with ALL modules on E90 but NOT E46, that suggests a "Datens issue" with the 1-click ISTA install. If the "source" for the ISTA Download can't be consulted, it would be easier to delete that version and install the "formerly-linked-by-BimmerGeeks" ISTA+ version found here:
https://mega.nz/file/a1wUmYCD#G0C3_H...o9uQ4EpxjI8oZs
As I understand, THAT version of ISTA requires a functioning installation of INPA BEFORE installing ISTA. I installed BMW Standard Tools/INPA months before installing ISTA, and ONLY installed ISTA after the October 2020 closure of NewTIS (I had downloaded the 9.98 GB Zipped Folder a year earlier, but NEVER installed it).
When you "UnZip" the compressed folder, a txt file with one page of installation instructions appears. Just follow that, and please let us know how it goes.
Another thing just occurred to me:
My ISTA installation will allow me to search & read "Documents" such as SSP wiring diagrams. I just enter Last-7 characters of VIN, program identifies vehicle type (Production Date, Engine, Trans, etc.) and provides documents for THAT specific vehicle, such as correct fuse numbers, etc.
That works for ANY E9x model for which I have tried it, several dozen different VIN-7's provided by others. It's in the Software on HD, and does NOT require connection to vehicle. It even works on my Desktop, that has never been connected to any vehicle (my BG K+DCAN cable is only ~ 5' ;-)
If your ISTA install allows you to search & read documents for your E92, but NOT for E46, that would be further indication of lack of Datens reference. As stated above I have NO Clue HOW one would/could add E46 Datens to your current installation.
George