Well, since no answer is given yet I'd might as well describe how I made this work. It's pretty simple although depending on the target system it can be tedious.
Using "-nostdinc" means that the standard system include paths will be skipped; other include-paths given with "-I" will of course still be searched for headers.
So, for the freestanding build target I create a folder 'include-freestanding-c89' and link the relevant system headers -- float.h, iso646.h, limits.h, stdarg.h and stddef.h -- there. Other headers might be included in these, depending on your platform, so you might have to do some research and set up more links (hence the tediousness if you need to do this for several target platforms).
The C89 directory can then be used as base for 'include-freestanding-c99', the extra headers to link are stdbool.h and stdint.h
The command-line to use is then
gcc -std=c89 -nostdinc -nostdlib -ffreestanding -I include-freestanding-c89
or
gcc -std=c99 -nostdinc -nostdlib -ffreestanding -I include-freestanding-c99
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