automake vs. GNU make

That isn't really necessary for variable names (that you don't need to reference later), only
the source and targets need to be qualified.  A fairly typical example:

# Define sources for this component:
MY_SRC = $(wildcard foo/*.c)
MY_OBJ = $(MY_SRC:.c=.o)
MY_TGT = foo/libfoo.a

# Additional flags and dependencies for building this component:
$(MY_OBJ): CPPFLAGS += -I foo
$(MY_TGT): $(MY_OBJ)

# Add these to the master Makefile's lists:
SOURCE += $(MY_SRC)
TARGET += $(MY_TGT)
CLEAN  += $(MY_OBJ)

The next component can reuse MY_SRC etc.  You wouldn't even need these variables, if you had
no need for target-specific variables or dependencies.  (But of course, you usually do).  If
you wanted to keep a reference to 'foo/libfoo.a', for use in other Makefiles, you might
replace MY_TGT with LIBFOO.

In short, you only need unique names for global variables; local ones can be overwritten.

You do need the component path ('foo' in this example) in a few spots, but it is trivial to
change that if the directory structure changes.