Fix missing time for some script functions in profiler

Fixes the issue by adding a mechanism by which the functions that were
previously disappearing can be profiled too. This is optional with
an editor setting, since collecting more information naturally slows the engine
further while profiling.

Fixes #23715, #40251, #29049

editor/debugger/script_editor_debugger.cpp

@@ -758,6 +758,7 @@ void ScriptEditorDebugger::_parse_message(const String &p_msg, uint64_t p_thread
 			int calls = frame.script_functions[i].call_count;
 			float total = frame.script_functions[i].total_time;
 			float self = frame.script_functions[i].self_time;
+			float internal = frame.script_functions[i].internal_time;
 
 			EditorProfiler::Metric::Category::Item item;
 			if (profiler_signature.has(signature)) {
@@ -782,6 +783,7 @@ void ScriptEditorDebugger::_parse_message(const String &p_msg, uint64_t p_thread
 			item.calls = calls;
 			item.self = self;
 			item.total = total;
+			item.internal = internal;
 			funcs.items.write[i] = item;
 		}
 
@@ -1097,7 +1099,9 @@ void ScriptEditorDebugger::_profiler_activate(bool p_enable, int p_type) {
 				// Add max funcs options to request.
 				Array opts;
 				int max_funcs = EDITOR_GET("debugger/profiler_frame_max_functions");
+				bool include_native = EDITOR_GET("debugger/profile_native_calls");
 				opts.push_back(CLAMP(max_funcs, 16, 512));
+				opts.push_back(include_native);
 				msg_data.push_back(opts);
 			}
 			_put_msg("profiler:servers", msg_data);