I think i want to write the tool myself, it turned out to be quite fun and its only for my personal usage.
I feel you, I do the same thing from time to time.
Do you use CMake?
If so, have you configured it to suit your projects so you dont have to keep coming back to changing any of its settings,
or do you find that from time to time that there are some settings that you would like to change?
I do, extensively. I sometimes have to change things, for instance to account for new dependencies or changes to the way they need to be linked as new versions are released. And really, in practice, your directory structure is probably not as fixed as you'd like it to be. Also, new platforms are not as straightforward as they should be, and generally require at least a little bit of custom code. I can deploy new clean projects using my game engine to Windows, Linux, iOS (simulator AND hardware), and OSX with my current build scripts, but getting to that point was not at all trivial...although that is the intention of CMake. I gather that adding support for Android will be another big hassle.
Im wondering if this is something that i should consider or, if id just have the tool generate the default files with my settings and if the user
wants to do any tweaks he can do it after the files have been generated.
Your approach could work, but you might as well just let them parameterize your tool in the first place with their desired settings. I use the same script to generate slightly different builds for the iOS simulator and iOS hardware:
cmake -DIOS_PLATFORM=SIMULATOR vs. cmake -DIOS_PLATFORM=OS
Of course, I can put these in different build trees, and I can rerun cmake to update those trees as project settings change, which certainly happens. It's not so hard to add basic command line arguments. I don't know enough about your exact use case to comment further. I've found CMake to be tremendously obtuse, so I have a hard time recommending it, it's just that at some point you might realize that your tool is just reinventing the wheel and have to concede defeat anyway (I'm not saying that that's the case here, yet )