Just have the one runlevels folder with OS includes.

runlevels.BSD/Makefile

@@ -1,5 +0,0 @@
-BOOT=		hostid net.lo0 newsyslog savecore syslogd
-DEFAULT=	local.rc mixer powerd 
-
-MK=		../mk
-include ${MK}/runlevels.mk

runlevels.FreeBSD/Makefile

@@ -1,4 +0,0 @@
-BOOT=	clock dumpon syscons
-
-MK=	../mk
-include ${MK}/runlevels.mk

runlevels.Linux/Makefile

@@ -1,5 +0,0 @@
-BOOT=		clock consolefont keymaps modules net.lo procfs
-DEFAULT=	hdparm
-
-MK=			../mk
-include ${MK}/runlevels.mk

runlevels.NetBSD/Makefile

@@ -1,4 +0,0 @@
-BOOT=	ttys
-
-MK=	../mk
-include ${MK}/runlevels.mk

runlevels/Makefile

@@ -7,4 +7,8 @@ BOOTDIR=	${LEVELDIR}/boot
 DEFAULTDIR=	${LEVELDIR}/default
 
 MK=		../mk
+include ${MK}/os.mk
+include Makefile.${OS}
+include Makefile.${SUBOS}
+
 include ${MK}/runlevels.mk

runlevels/Makefile.BSD

@@ -0,0 +1,2 @@
+BOOT+=		hostid net.lo0 newsyslog savecore syslogd
+DEFAULT+=	local.rc mixer powerd 

runlevels/Makefile.FreeBSD

@@ -0,0 +1 @@
+BOOT+=	clock dumpon syscons

runlevels/Makefile.Linux

@@ -0,0 +1,2 @@
+BOOT+=		clock consolefont keymaps modules net.lo procfs
+DEFAULT+=	hdparm

runlevels/Makefile.NetBSD

@@ -0,0 +1 @@
+BOOT+=	ttys