Thank you for the report and I am sorry to hear about that!
I checked with the latest update for Archicad 25 (5010), and here I found that all MVOs are saved to the module file. Regarding the building materials, I tested it as far back as AC23, and they all behave the same way: unused building materials in the module file won't have a classification assigned to them. Could you please let me know which exact version did you find unused materials not being exported to module?
File > External Content > Save Selection as Module
If we create MOD file using above method then MVO goes missing and only one default MVO appears as seen in attached screenshot.
As you suggested all materials are getting transferred to MOD file in Archicad 25. For now i could only check in AC24 7000 version, and material get exported to MOD but become unclassified. It was one of the previous version of AC24 where, only used materials were getting exported to MOD, but as we have now upgraded to AC 25 in all machines i can not find out for sure which AC24 version was it, where only used material were getting exported to MOD.
I believe what you experienced here is intentional. A Module format file is a simplified type of Archicad file, which can be placed as a Hotlink Module or merged into a project. A .mod file is not meant to be used as a working file but more as a courier of information, thus we want to minimize the unnecessary data saved into it. With Save selection as module function, this reduces even more data. MVO for example is not saved out.
All in all, the module is meant to be a container. Could you please let us know why you need MVO exported to the modules?
Regarding unused building materials in module: I tried all different builds of Archicad 24. None of which showed the problem as you described. Anyhow, if it is true, then it's likely to be a bug. Such a big change in attribute management in hotlink modules is unlikely to happen through an update. All recent Archicad versions (even AC23) showed the same behavior, so I think what you described might happen on a different version.
I pointed out MVO missing only because, everything else from visual settings bottom bar remains intact, like Layer combinations, Graphic Overrides, Renovation Filters. I noticed that only MVO and Pensets go missing when MOD is created by selecting elements and saving them as MOD.
Just could not find any logic in why should only MVO and Penset be missing in MOD so checked here.
Also, as a part of the modeling process we do have to work on MOD files and updated the same for repetitive layout.