diff --git a/src/mutation_data.cpp b/src/mutation_data.cpp
index bd3750e81e631..a0c3d39a1a25e 100644
--- a/src/mutation_data.cpp
+++ b/src/mutation_data.cpp
@@ -650,6 +650,8 @@ void mutation_branch::check_consistency()
 {
     for( const mutation_branch &mdata : get_all() ) {
         const trait_id &mid = mdata.id;
+        const mod_id &trait_source = mdata.src.back().second;
+        const bool basegame_trait = trait_source.str() == "dda";
         const std::optional<scenttype_id> &s_id = mdata.scent_typeid;
         const std::map<species_id, int> &an_id = mdata.anger_relations;
         for( const auto &style : mdata.initial_ma_styles ) {
@@ -676,10 +678,13 @@ void mutation_branch::check_consistency()
         if( s_id && !s_id.value().is_valid() ) {
             debugmsg( "mutation %s refers to undefined scent type %s", mid.c_str(), s_id.value().c_str() );
         }
+        // Suppress these onload warnings for overlapping mods
         for( const trait_id &replacement : mdata.replacements ) {
             const mutation_branch &rdata = replacement.obj();
+            bool suppressed = rdata.src.back().second != trait_source && !basegame_trait;
             for( const mutation_category_id &cat : rdata.category ) {
-                if( std::find( mdata.category.begin(), mdata.category.end(), cat ) == mdata.category.end() ) {
+                if( std::find( mdata.category.begin(), mdata.category.end(), cat ) == mdata.category.end() &&
+                    !suppressed ) {
                     debugmsg( "mutation %s lacks category %s present in replacement mutation %s", mid.c_str(),
                               cat.c_str(), replacement.c_str() );
                 }
@@ -691,27 +696,28 @@ void mutation_branch::check_consistency()
             }
             const mutation_branch &adata = addition.obj();
             bool found = false;
+            bool suppressed = adata.src.back().second != trait_source && !basegame_trait;
             for( const mutation_category_id &cat : adata.category ) {
                 found = found ||
                         std::find( mdata.category.begin(), mdata.category.end(), cat ) != mdata.category.end();
             }
-            if( !found ) {
+            if( !found && !suppressed ) {
                 debugmsg( "categories in mutation %s don't match any category present in additive mutation %s",
                           mid.c_str(), addition.c_str() );
             }
         }
 
-        // Suppress this check for trait/prereq combos from different mod sources
         for( const mutation_category_id &cat_id : mdata.category ) {
             if( !mdata.prereqs.empty() ) {
                 bool found = false;
+                bool suppressed = false;
                 for( const trait_id &prereq_id : mdata.prereqs ) {
                     const mutation_branch &prereq = prereq_id.obj();
+                    suppressed = suppressed || ( prereq.src.back().second != trait_source && !basegame_trait );
                     found = found ||
-                            std::find( prereq.category.begin(), prereq.category.end(), cat_id ) != prereq.category.end() ||
-                            mdata.src.end()->second != prereq.src.end()->second;
+                            std::find( prereq.category.begin(), prereq.category.end(), cat_id ) != prereq.category.end();
                 }
-                if( !found ) {
+                if( !found && !suppressed ) {
                     debugmsg( "mutation %s is in category %s but none of its slot 1 prereqs have this category",
                               mid.c_str(), cat_id.c_str() );
                 }
@@ -719,13 +725,14 @@ void mutation_branch::check_consistency()
 
             if( !mdata.prereqs2.empty() ) {
                 bool found = false;
+                bool suppressed = false;
                 for( const trait_id &prereq_id : mdata.prereqs2 ) {
                     const mutation_branch &prereq = prereq_id.obj();
+                    suppressed = suppressed || ( prereq.src.back().second != trait_source && !basegame_trait );
                     found = found ||
-                            std::find( prereq.category.begin(), prereq.category.end(), cat_id ) != prereq.category.end() ||
-                            mdata.src.end()->second != prereq.src.end()->second;
+                            std::find( prereq.category.begin(), prereq.category.end(), cat_id ) != prereq.category.end();
                 }
-                if( !found ) {
+                if( !found && !suppressed ) {
                     debugmsg( "mutation %s is in category %s but none of its slot 2 prereqs have this category",
                               mid.c_str(), cat_id.c_str() );
                 }