Setting -R through MAKEFLAGS should set -r, just like -R on the command line sets -r.

$ cat makefile
MAKEFLAGS:=-R
all: hello.o
$ make --debug=implicit 2>&1 |tail -10
    Trying implicit prerequisite 'RCS/hello.mod,v'.
    Trying pattern rule with stem 'hello.mod'.
    Trying implicit prerequisite 'RCS/hello.mod'.
    Trying pattern rule with stem 'hello.mod'.
    Trying implicit prerequisite 's.hello.mod'.
    Trying pattern rule with stem 'hello.mod'.
    Trying implicit prerequisite 'SCCS/s.hello.mod'.
   No implicit rule found for 'hello.o'.
  Must remake target 'hello.o'.
make: *** No rule to make target 'hello.o', needed by 'all'.  Stop.
$

Same example with this patch.

$ make --debug=implicit 2>&1 |tail -10
Updating makefiles....
Updating goal targets....
 File 'all' does not exist.
 Looking for an implicit rule for 'all'.
 No implicit rule found for 'all'.
   File 'hello.o' does not exist.
   Looking for an implicit rule for 'hello.o'.
   No implicit rule found for 'hello.o'.
  Must remake target 'hello.o'.
make: *** No rule to make target 'hello.o', needed by 'all'.  Stop.
$