This is an issue and solved already. In Godot 4.4 and 4.5 ( I only tested this 2 versions )
If you run the main scence, consel logs that:
Embedded window resize can't be disabled.
Embedded window can't become on top.
......
If in this case, please click off this checkbox Embedded Game on Next Play in debug scence.

Then in next run, it gonna workout as normal.