This is way out of my wheelhouse, but ... I am will be needing to look for a diagramming tool myself, and I refuse to use a proprietary Microsoft product, so I googled for: Visio alternative free and found:

The 13 Best Free Alternatives to Microsoft Visio https://www.online-tech-tips.com/software-reviews/the-13-best-free-alternatives-to-microsoft-visio/

and

Top 10 Microsoft Visio Alternatives And Competitors In 2022 https://www.softwaretestinghelp.com/visio-alternatives/

and

Alternatives to Gliffy https://stackshare.io/gliffy/alternatives

The ones that kept recurring among my search were: Microsoft Visio, and LucidCharts

Here's an article describing Layers with LucidCharts:

Interactive Diagrams: 3 Ways to Use Hotspots and Layers in Lucidchart https://www.lucidchart.com/blog/interactive-diagrams-3-ways-to-use-hotspots-and-layers

Also

Work with layers in diagrams.net https://www.diagrams.net/doc/layers

Miro looks nice, ... but does not have Layers.

I had used Dia some years ago. I liked Visio better. No idea if Dia has layers though I saw something called "Layer objects".

That was the extent of my research so no idea what others have support for layers.

Hope this helps.