No matter which way you work it, easymod isn't going to be 100% foo-proof installing MODs.
Using 'keywords' or line numbers won't help much better - if you modify a php/tpl file and add code to it, you're adding more lines to the file.
So if you try to install a MOD using a line number as guidance, it could fail and drastically muck up your files as the code it needs may have been moved a few lines down
I think they way it works just now if just fine.
Best thing to do is to use the'preview' when installing. That way if you install is going to fail on a file or 2, you can manually edit those parts, then remove the lines from the install file
I'm not trying to dismiss you completely here, just giving my view. Please feel free to have a look over at area51.phpbb.com - that's the base for all easymod support. Maybe evern post your question there to Nuttzy and see what he thinks 8)