Addition: this bug occurs after restarting the editor (no reset buttons). After saving the scene, the inspector starts working correctly again.

I could not reproduce the bug with saving default values for nodes. Only for resources ([sub_resource]), but seems to be an old bug not related to @tool.

Just a few pictures to illustrate what happens when adding @tool later, with numerical properties:

# keep commented out for now
#@tool
class_name Arena
extends Node2D

@export var tilemap_cell_size: float = 16.0
@export var tilemap_width: int = 72
@export var tilemap_height: int = 37

Create Arena node, change properties to see revert arrow button appear:

Then uncomment @tool at the top of the script. Issue won't appear at once, but after editor reboot, revert buttons disappeared:

Oddly enough, in the reverse way, if you temporarily comment out @tool, the reset to default buttons will reappear immediately, and not disappear even if you uncomment @tool until next reboot.

So my current workaround is to comment @tool once during my work session if I need to revert the properties at some point.