diff --git a/src/clangsa/GCChecker.cpp b/src/clangsa/GCChecker.cpp
index 9f7a5e22d22b4..086d925802f63 100644
--- a/src/clangsa/GCChecker.cpp
+++ b/src/clangsa/GCChecker.cpp
@@ -191,15 +191,6 @@ class GCChecker
     }
     return f(TD->getName());
   }
-  static bool isValueCollection(QualType QT) {
-    if (QT->isPointerType() || QT->isArrayType())
-      return isValueCollection(
-          clang::QualType(QT->getPointeeOrArrayElementType(), 0));
-    const TagDecl *TD = QT->getUnqualifiedDesugaredType()->getAsTagDecl();
-    if (!TD)
-      return false;
-    return declHasAnnotation(TD, "julia_rooted_value_collection");
-  }
   template <typename callback>
   static SymbolRef walkToRoot(callback f, const ProgramStateRef &State,
                               const MemRegion *Region);
@@ -768,8 +759,7 @@ static bool isMutexUnlock(StringRef name) {
 #endif
 
 bool GCChecker::isGCTrackedType(QualType QT) {
-  return isValueCollection(QT) ||
-         isJuliaType(
+  return isJuliaType(
              [](StringRef Name) {
                if (Name.endswith_lower("jl_value_t") ||
                    Name.endswith_lower("jl_svec_t") ||
diff --git a/src/subtype.c b/src/subtype.c
index 9f6f6cb0add67..19a3e3286982b 100644
--- a/src/subtype.c
+++ b/src/subtype.c
@@ -968,17 +968,6 @@ static int check_vararg_length(jl_value_t *v, ssize_t n, jl_stenv_t *e)
 
 static int forall_exists_equal(jl_value_t *x, jl_value_t *y, jl_stenv_t *e);
 
-struct subtype_tuple_env {
-    jl_datatype_t *xd, *yd;
-    jl_value_t *lastx, *lasty;
-    size_t lx, ly;
-    size_t i, j;
-    int vx, vy;
-    jl_value_t *vtx;
-    jl_value_t *vty;
-    jl_vararg_kind_t vvx, vvy;
-} JL_ROOTED_VALUE_COLLECTION;
-
 static int subtype_tuple_varargs(
     jl_vararg_t *vtx, jl_vararg_t *vty,
     size_t vx, size_t vy,
@@ -1092,7 +1081,7 @@ static int subtype_tuple_tail(jl_datatype_t *xd, jl_datatype_t *yd, int8_t R, jl
 {
     size_t lx = jl_nparams(xd);
     size_t ly = jl_nparams(yd);
-    size_t i = 0, j = 0, vx = 0, vy = 0, x_reps = 0;
+    size_t i = 0, j = 0, vx = 0, vy = 0, x_reps = 1;
     jl_value_t *lastx = NULL, *lasty = NULL;
     jl_value_t *xi = NULL, *yi = NULL;
 
@@ -1142,21 +1131,17 @@ static int subtype_tuple_tail(jl_datatype_t *xd, jl_datatype_t *yd, int8_t R, jl
             return !!vx;
 
         xi = vx ? jl_unwrap_vararg(xi) : xi;
-        int x_same = lastx && jl_egal(xi, lastx);
-        if (vy) {
-            yi = jl_unwrap_vararg(yi);
-            // keep track of number of consecutive identical types compared to Vararg
-            if (x_same)
-                x_reps++;
-            else
-                x_reps = 1;
-        }
+        yi = vy ? jl_unwrap_vararg(yi) : yi;
+        int x_same = vx > 1 || (lastx && obviously_egal(xi, lastx));
+        int y_same = vy > 1 || (lasty && obviously_egal(yi, lasty));
+        // keep track of number of consecutive identical subtyping
+        x_reps = y_same && x_same ? x_reps + 1 : 1;
         if (x_reps > 2) {
-            // an identical type on the left doesn't need to be compared to a Vararg
+            // an identical type on the left doesn't need to be compared to the same
             // element type on the right more than twice.
         }
         else if (x_same && e->Runions.depth == 0 &&
-            ((yi == lasty && !jl_has_free_typevars(xi) && !jl_has_free_typevars(yi)) ||
+            ((y_same && !jl_has_free_typevars(xi) && !jl_has_free_typevars(yi)) ||
              (yi == lastx && !vx && vy && jl_is_concrete_type(xi)))) {
             // fast path for repeated elements
         }
@@ -3073,9 +3058,6 @@ static jl_value_t *intersect_tuple(jl_datatype_t *xd, jl_datatype_t *yd, jl_sten
                     (yb && jl_is_long(yb->lb) && ly-1+jl_unbox_long(yb->lb) != len)) {
                     res = jl_bottom_type;
                 }
-                else if (param == 2 && jl_is_unionall(xi) != jl_is_unionall(yi)) {
-                    res = jl_bottom_type;
-                }
                 else {
                     if (xb) set_var_to_const(xb, jl_box_long(len-lx+1), yb);
                     if (yb) set_var_to_const(yb, jl_box_long(len-ly+1), xb);
diff --git a/src/support/analyzer_annotations.h b/src/support/analyzer_annotations.h
index 3e577e6b45483..69827e4d77f37 100644
--- a/src/support/analyzer_annotations.h
+++ b/src/support/analyzer_annotations.h
@@ -22,7 +22,6 @@
 #define JL_ALWAYS_LEAFTYPE JL_GLOBALLY_ROOTED
 #define JL_ROOTS_TEMPORARILY __attribute__((annotate("julia_temporarily_roots")))
 #define JL_REQUIRE_ROOTED_SLOT __attribute__((annotate("julia_require_rooted_slot")))
-#define JL_ROOTED_VALUE_COLLECTION __attribute__((annotate("julia_rooted_value_collection")))
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -46,7 +45,6 @@ extern "C" {
 #define JL_ALWAYS_LEAFTYPE
 #define JL_ROOTS_TEMPORARILY
 #define JL_REQUIRE_ROOTED_SLOT
-#define JL_ROOTED_VALUE_COLLECTION
 #define JL_GC_PROMISE_ROOTED(x) (void)(x)
 #define jl_may_leak(x) (void)(x)
 
diff --git a/test/subtype.jl b/test/subtype.jl
index 674608c4d0451..c0fc41abda174 100644
--- a/test/subtype.jl
+++ b/test/subtype.jl
@@ -2426,6 +2426,9 @@ end
 
 @test !(Tuple{Any, Any, Any} <: Tuple{Any, Vararg{T}} where T)
 
+# issue #39967
+@test (NTuple{27, T} where {S, T<:Union{Array, Array{S}}}) <: Tuple{Array, Array, Vararg{AbstractArray, 25}}
+
 abstract type MyAbstract47877{C}; end
 struct MyType47877{A,B} <: MyAbstract47877{A} end
 let A = Tuple{Type{T}, T} where T,