Headless doctool run generate different docs than normal run

[qarmin]

Godot version

4.0.dev.custom_build. bf322ba

System information

Ubuntu 21.04 - Nvidia GTX 970, Gnome shell 3.38 X11

Issue description

Git diff

diff --git a/doc/classes/GPUParticles2D.xml b/doc/classes/GPUParticles2D.xml
index 72bd6a6411..51056bf843 100644
--- a/doc/classes/GPUParticles2D.xml
+++ b/doc/classes/GPUParticles2D.xml
@@ -34,7 +34,7 @@
 		<member name="draw_order" type="int" setter="set_draw_order" getter="get_draw_order" enum="GPUParticles2D.DrawOrder" default="1">
 			Particle draw order. Uses [enum DrawOrder] values.
 		</member>
-		<member name="emitting" type="bool" setter="set_emitting" getter="is_emitting" default="true">
+		<member name="emitting" type="bool" setter="set_emitting" getter="is_emitting" default="false">
 			If [code]true[/code], particles are being emitted.
 		</member>
 		<member name="explosiveness" type="float" setter="set_explosiveness_ratio" getter="get_explosiveness_ratio" default="0.0">
diff --git a/doc/classes/GPUParticles3D.xml b/doc/classes/GPUParticles3D.xml
index 0bed561de3..af0a756e46 100644
--- a/doc/classes/GPUParticles3D.xml
+++ b/doc/classes/GPUParticles3D.xml
@@ -76,7 +76,7 @@
 		</member>
 		<member name="draw_skin" type="Skin" setter="set_skin" getter="get_skin">
 		</member>
-		<member name="emitting" type="bool" setter="set_emitting" getter="is_emitting" default="true">
+		<member name="emitting" type="bool" setter="set_emitting" getter="is_emitting" default="false">
 			If [code]true[/code], particles are being emitted.
 		</member>
 		<member name="explosiveness" type="float" setter="set_explosiveness_ratio" getter="get_explosiveness_ratio" default="0.0">
diff --git a/doc/classes/ProjectSettings.xml b/doc/classes/ProjectSettings.xml
index eec06d6f82..971f88fed2 100644
--- a/doc/classes/ProjectSettings.xml
+++ b/doc/classes/ProjectSettings.xml
@@ -275,9 +275,6 @@
 		<member name="audio/buses/default_bus_layout" type="String" setter="" getter="" default="&quot;res://default_bus_layout.tres&quot;">
 			Default [AudioBusLayout] resource file to use in the project, unless overridden by the scene.
 		</member>
-		<member name="audio/driver/driver" type="String" setter="" getter="">
-			Specifies the audio driver to use. This setting is platform-dependent as each platform supports different audio drivers. If left empty, the default audio driver will be used.
-		</member>
 		<member name="audio/driver/enable_input" type="bool" setter="" getter="" default="false">
 			If [code]true[/code], microphone input will be allowed. This requires appropriate permissions to be set when exporting to Android or iOS.
 		</member>
@@ -1768,18 +1765,10 @@
 			If [code]true[/code], the texture importer will import VRAM-compressed textures using the S3 Texture Compression algorithm. This algorithm is only supported on desktop platforms and consoles.
 			[b]Note:[/b] Changing this setting does [i]not[/i] impact textures that were already imported before. To make this setting apply to textures that were already imported, exit the editor, remove the [code].godot/imported/[/code] folder located inside the project folder then restart the editor (see [member application/config/project_data_dir_name]).
 		</member>
-		<member name="rendering/vulkan/descriptor_pools/max_descriptors_per_pool" type="int" setter="" getter="" default="64">
-		</member>
 		<member name="rendering/vulkan/rendering/back_end" type="int" setter="" getter="" default="0">
 		</member>
 		<member name="rendering/vulkan/rendering/back_end.mobile" type="int" setter="" getter="" default="1">
 		</member>
-		<member name="rendering/vulkan/staging_buffer/block_size_kb" type="int" setter="" getter="" default="256">
-		</member>
-		<member name="rendering/vulkan/staging_buffer/max_size_mb" type="int" setter="" getter="" default="128">
-		</member>
-		<member name="rendering/vulkan/staging_buffer/texture_upload_region_size_px" type="int" setter="" getter="" default="64">
-		</member>
 		<member name="rendering/xr/enabled" type="bool" setter="" getter="" default="false">
 			If [code]true[/code], XR support is enabled in Godot, this ensures required shaders are compiled.
 		</member>

this is(probably) needed by #51950 because without it looks that xvfb crashes

Steps to reproduce

godot --doctool . output behave different than godot --doctool . --headless

Minimal reproduction project

No response