I'm not really knowledgeable enough about autoconf to be absolute certain but test seem to indicate it does.
The test performed (on a system without `freetype-config`):
* Using a pristine repository copy (no manual alterations [1])
* Run `autoconf` -> output message includes: "checking for library containing FT_Init_FreeType... -lfreetype"
* Run `./configure` -> Verified `configure.default` includes: "USE_FREETYPE = 1"
* Run `make`
This creates a working binary, with only one catch. In order to compile successfully i had to edit the Makefile (line 14)
from
FREETYPE_CONFIG ?= freetype-config
to
FREETYPE_CONFIG ?= pkg-config freetype2
As for the breakage of other software. This will most likely be the case for all distributions that do not take special precautions when building freetype2 (e.g. using the flag '--enable-freetype-config' for versions >= 2.9.1).
More information:
* The reason why the developers of freetype2 dropped it (for default builds) is mentioned in
this bugreport* They also warn against it's usage in
one of their basic tutorials (last sentence of the first step).
Hope this helps a bit
[1] With the exception of the Makefile edit