Interesting, but hardly "standard" 
Unofficial files are expected to be in LDraw\Unofficial and the rest of your installation mimics the "old" C:\LDraw setup which also contained an "Apps" folder inside which different versions of MLCad could live side by side without any problem.
I still need to get the hang of SR 3D so I can't comment on its folder structure, but maybe you have experienced something similar to what I described concerning LDCad where I couldn't find files I had saved because Windows wouldn't let the program save the files to the default location and diverted them to a user specific location buried deep in the system. This was solved by unchecking the "read-only" option in the properties for the LDcad installation folder.
Bottom line: installing to C:\Program Files (x86) causes a lot of issues unless the folder is correctly made accessible by the program. If that cannot be done, maybe a different solution needs to be found.
Unofficial files are expected to be in LDraw\Unofficial and the rest of your installation mimics the "old" C:\LDraw setup which also contained an "Apps" folder inside which different versions of MLCad could live side by side without any problem.
I still need to get the hang of SR 3D so I can't comment on its folder structure, but maybe you have experienced something similar to what I described concerning LDCad where I couldn't find files I had saved because Windows wouldn't let the program save the files to the default location and diverted them to a user specific location buried deep in the system. This was solved by unchecking the "read-only" option in the properties for the LDcad installation folder.
Bottom line: installing to C:\Program Files (x86) causes a lot of issues unless the folder is correctly made accessible by the program. If that cannot be done, maybe a different solution needs to be found.