I know nothing about autotools, so I should probably stop talking, but not quite yet.
You say GNUMAKEFLAGS+=-r is "invalid syntax" but I don't know quite how to read that. It's not invalid in the sense of causing an error, it's just that it would be invisible to any non-GNU make program so presumably that's what you mean. But the thing is, I don't believe other make programs are reactive to MAKEFLAGS being set within the makefile. At least, it's been a long time since I read POSIX but I don't think it's required. My assumption may be wrong but if not, setting MAKEFLAGS would be a NOP in non-GNU makes anyway. Except that it would take effect in recursive invocations but that complicates things further.
Anyway, I really should stop talking since I know zero about automake.
David