As long as you don't have your Steam folder in the C:\Program Files (x86) folder and you are running RW_Tools as administrator, there should be no problem altering/saving .bin files with RW_Tools. There should be no read-only files in TS2015 unless you are using 7zip (the version you download from the web) to extract files from within the .ap files.
If you use RW_Tools to extract files from within .ap files, then they will automatically be made read/write as it uses a different version of 7zip and automatically makes extracted files read/write.
Note that there is an option in the RW_Tools Options menu to make all files read/write if you have some which are not.
Mike