diff --git a/src/libslic3r/GCode/WipeTower.cpp b/src/libslic3r/GCode/WipeTower.cpp
index 5834937169..790c0d9d73 100644
--- a/src/libslic3r/GCode/WipeTower.cpp
+++ b/src/libslic3r/GCode/WipeTower.cpp
@@ -1350,7 +1350,7 @@ public:
             buffer += "M400\n";
         buffer += "M104";
         if (target_extruder != -1)
-            buffer += (" T" + std::to_string(m_physical_extruder_map[target_extruder]));
+            buffer += (" T" + std::to_string(physical_extruder_for(target_extruder)));
         buffer += " S" + std::to_string(target_temp) + " N0"; // N0 means the gcode is generated by slicer
         if (!comment.empty()) buffer += " ;" + comment;
         buffer += '\n';
@@ -1362,7 +1362,7 @@ public:
     {
         std::string buffer = "M109";
         if (target_extruder != -1)
-            buffer += (" T" + std::to_string(m_physical_extruder_map[target_extruder]));
+            buffer += (" T" + std::to_string(physical_extruder_for(target_extruder)));
         buffer += " S" + std::to_string(target_temp) + " N0"; // N0 means the gcode is generated by slicer
         if (!comment.empty()) buffer += " ;" + comment;
         buffer += '\n';
@@ -1382,6 +1382,15 @@ public:
     void set_multi_nozzle_group_result(const MultiNozzleUtils::LayeredNozzleGroupResult *multi_nozzle_group_result) { m_multi_nozzle_group_result = multi_nozzle_group_result; }
     void set_physical_extruder_map(const std::vector<int> &physical_extruder_map) { m_physical_extruder_map = physical_extruder_map; }
 
+    // physical_extruder_map defaults to the single element {0} and is only widened to one entry
+    // per extruder on IMEX printers, so indexing it by tool is out of range on any other
+    // multi-extruder machine. Fall back to the tool's own index, matching the bounds-checked
+    // form GCodeProcessor uses for the same map.
+    int physical_extruder_for(int tool) const
+    {
+        return tool >= 0 && tool < (int) m_physical_extruder_map.size() ? m_physical_extruder_map[tool] : tool;
+    }
+
 private:
     std::string set_normal_acceleration() {
         std::vector<unsigned int> accelerations = m_is_first_layer ? m_first_layer_normal_accelerations : m_normal_accelerations;
diff --git a/src/libslic3r/Preset.cpp b/src/libslic3r/Preset.cpp
index e3ac3a75df..211de76a6c 100644
--- a/src/libslic3r/Preset.cpp
+++ b/src/libslic3r/Preset.cpp
@@ -733,12 +733,6 @@ void Preset::save(DynamicPrintConfig* parent_config)
                 ConfigOptionVectorBase* opt_vec_inherit = static_cast<ConfigOptionVectorBase*>(parent_config->option(option));
                 if (opt_vec_src->size() == 1)
                     opt_dst->set(opt_src);
-                else if (opt_vec_src->size() != opt_vec_inherit->size()) {
-                    // Size mismatch (e.g. new multi-extruder profile inheriting from a
-                    // single-extruder base): nil-delta encoding requires matching sizes,
-                    // so fall back to storing the full vector.
-                    opt_dst->set(opt_src);
-                }
                 else if (key_set1->find(option) != key_set1->end()) {
                     opt_vec_dst->set_with_nil(opt_vec_src, opt_vec_inherit, 1);
                 }
@@ -1905,12 +1899,6 @@ Preset* PresetCollection::get_preset_differed_for_save(Preset& preset)
                 ConfigOptionVectorBase* opt_vec_inherit = static_cast<ConfigOptionVectorBase*>(parent_preset->config.option(option));
                 if (opt_vec_src->size() == 1)
                     opt_dst->set(opt_src);
-                else if (opt_vec_src->size() != opt_vec_inherit->size()) {
-                    // Size mismatch (e.g. new multi-extruder profile inheriting from a
-                    // single-extruder base): nil-delta encoding requires matching sizes,
-                    // so fall back to storing the full vector.
-                    opt_dst->set(opt_src);
-                }
                 else if (key_set1->find(option) != key_set1->end()) {
                     opt_vec_dst->set_with_nil(opt_vec_src, opt_vec_inherit, 1);
                 }
diff --git a/src/libslic3r/PrintApply.cpp b/src/libslic3r/PrintApply.cpp
index 3d1fc8f16c..579c5e5747 100644
--- a/src/libslic3r/PrintApply.cpp
+++ b/src/libslic3r/PrintApply.cpp
@@ -1313,7 +1313,19 @@ Print::ApplyStatus Print::apply(const Model &model, DynamicPrintConfig new_full_
     // Fill in physical_extruder_map when the printer profile has not authored one. It has one
     // entry per logical extruder, so it is sized from the nozzle count -- not from
     // printer_extruder_id, which is indexed by variant slot.
-    {
+    //
+    // IMEX printers only. physical_extruder_map carries two readings in this tree (see
+    // IMEXHelpers.hpp): the IMEX paths need one entry per logical extruder, the inherited BBL
+    // paths read it through the clamping get_at(), which collapses every logical extruder to
+    // physical 0 while the profile default is the single-element {0}. Deriving the identity
+    // unconditionally would impose the IMEX reading on printers that mean the other one and
+    // change what they emit -- {first_tools}/{first_filaments}/{first_non_support_*} and
+    // {most_used_physical_extruder_id}/{curr_physical_extruder_id} in custom start G-code, plus
+    // the `; physical_extruder_map =` line in the G-code config block -- for every multi-nozzle
+    // profile that never authored a map. Non-IMEX printers therefore keep the config value
+    // exactly as it arrives, which is what upstream slices with.
+    const auto* is_imex_opt = new_full_config.option<ConfigOptionBool>("is_imex");
+    if (is_imex_opt && is_imex_opt->value) {
         auto* pem = new_full_config.option<ConfigOptionInts>("physical_extruder_map", true);
         if (pem) {
             pem->values = effective_physical_extruder_map(pem, extruder_count).values;