Put the commands at the start of menuconfig and the toybox library options at the end. (Aesthetic tweak.)
diff --git a/Config.in b/Config.in
index 02137d8..835e703 100644
--- a/Config.in
+++ b/Config.in
@@ -1,5 +1,11 @@
mainmenu "ToyBox Configuration"
+
+source generated/Config.probed
+source generated/Config.in
+
+comment ""
+
menu "Toybox global settings"
config TOYBOX
@@ -43,9 +49,3 @@
Enable extra checks for debugging purposes.
endmenu
-
-source generated/Config.probed
-
-comment ""
-
-source generated/Config.in