I am very familiar with embedded stuff, and this whole system was built precisely because of that. Some people are developing in visual studio so give them a good visual studio project that works well, some are working with a proprietary garbage toolchains, so you need to let them write makefiles and have enough flexibility to let them encode how to do that in the build system (e.g. all the different quirks you get for figuring out header file dependencies). The policy I used was "every toolchains needs some lowest common denominator support" and then "once you have that, let every toolchains be as good as possible with equivalences given abstractions". It did appear to work.
I think you may have misinterpreted me on the multiple build system thing. There is one build system and it produces files that each ide/toolchains can work with. So it can make xcode, visual studio, makefile, etc. No one edits those by hand, just like cmake, gyp, etc