I think you are still confused - it hasn't helped that you really didn't explain yourself properly.
There is no change (and no planned change) to the way source and object file names are handled. The way I've described is (more or less) how the tools in RISC OS have always worked.
"having to change the directory structure". But there are tools to automate this. If you really must, you can turn if off, but you will cause problems for yourself, unless all your source and header files are in the same format.