The Windows registry vs. INI files is surprisingly pro-registry.
First of all, using the Registry does not actually *fix* any issues with multiple instances that you can't fix pretty easily with INI files. In particular, the contention over the config data is the easy part of the problem. There's an inherent messy ambiguity with settings and multiple instances. If I change settings in instance 1 do I want those to be immediately reflected in instance 2? If so, the only way to fix this is to have all instances constantly checking for new settings (or get some notification). This problem is exactly the same with the registry or INI files. Sure the registry gives you nice safe atomic writes, but you can implement that yourself easily enough, or you could use an off the shelf database. So that is really not much of an argument. In fact, getting changes across instances with INI files could be done pretty neatly using a file change notification to cause reloads (I'm not sure if Windows provides a similar watcher notification mechanism for registry changes). (the system that most people use of dumping settings changes on program exit is equally broken with the registry or INI files).
Second, storing things like last dialog positions and dumping structs and such is not really appropriate for INI files (or really even for the registry for that matter). The INI file is for things that the user might want to edit by hand, or copy to other machines, or whatever. That other junk is really a logically separate type of data. It's like the NCB in MSVC, which we all know you want to just wipe out from time to time. (in fact making it separate is nice because if I accidentally get my last dialog position off in outer space I can just delete that data). I think the official nice Win32 way to store this data is off in AppData somewhere, but I don't love that either.
Third, the benefits of the INI are massive and understated. 1. text editting is in fact a huge benefit over the registry. It lets you see all the options and edit them in a tool that is friendly and familiar. 2. it lets you do all the things you would do normally on files - eg. I can easily email my INI to friends, I can save backups of settings I made for some purpose, hell I can munge the INI from batch files, I can easily zip it up to save old versions, etc.
And this last one is by far the most important - making programs be "transportable" - that is, they rely on nothing but stuff in dirs under them - is just a massive win. It lets me rearrange my disk, copy programs around without running installers, save versions of programs, etc.
Back in the DOS days, whenever I finished a code project, we would make tape backups (lol tape) of the code * and all the compilers used to build it *. To do that all you had to do was include the dir containing the compiler. Five years later we could pull out projects that used some bizarro compilers that we didn't have any more, and it would all just work because they were fully transportable. The win of that is so massive it dominates the convenience of the registry for the developer.
Which brings us to the most important part : the convenience for the developer is not the issue here! It's what would be nicer for the user. And there INI is just all win. If it's more work for the developer to make that work, we should do that work.