Saving Modern sites (while do-able) is not supported.
The first hint that it’s not supported is the fact that the link “Save This Site As Template” is missing. And as history shows us, if it’s missing , it’s missing for a reason: It’s not supported to save the site as template. Think about Publishing sites, Communication sites, etc.
(Expand Resolve Common problems and scroll down to the section “The Save site template command is not available”)
And the what other types of sites do not support save as template , see here for the sites that have publishing features enabled by default ( and therefore not save-able as template)
Now, Modern sites: somewhat not obvious but here it is :
Shortening bolding and coloring the relevant parts:
What’s not supported on “modern” team sites:
- Custom master pages; more extensive branding will be supported later using alternative options.
- Changing “modern” site to use “classic” seattle.master or oslo.master.
- Custom page layouts; we are looking to have support for multiple canvases in the future.
- Enabling site or site collection scoped publishing features; technically, features can be currently activated, but this is not a supported configuration.
- “Modern” subsites; subsites created on “modern” team sites use the “classic” experience, but you can change the user experience to be similar to “modern” sites.
- Ability to control available subsite template options.
- “Classic” publishing features (WCM).
- Activation of community feature or creation of community subsites under “modern” team site.
- Saving site as a template. Also not supported for sub sites in site collections which root site is a group associated team site or communication site.