Since SQL Server 2025 is fairly fresh, it might be a bug that has not yet been addressed.
I'd recommend making MS aware of this.
The restart scenario specifically sounds like SQL Server 2025 is having a hard time bringing that many databases online. You might want to check if Event Viewer has any relevant entries during that timeframe.
That being said, I can't say I've ever expected to read the following sentence:
Currently we have several servers running SQL Server 2022 Express each with around 3,000 databases.
