Disk Utility has never been a good app to clone a macOS boot drive even years ago before the new security restrictions built into macOS 11.x+. In theory it is possible, but when I've tried it in the past it would not always work. In fact sometimes I find Disk Utility even has problems making an image of a large folder.
As @P. Phillips mentioned the two macOS apps which have been around for years which have been great for making a clone of a macOS boot drive including the two APFS volumes (system & data) plus the hidden recovery partition/volume as well (at least with CCC).
However, with recent updates to macOS 12.x Monterey, Apple has been making new changes which have affected the ability of these apps to clone a macOS boot volume. Basically being able to clone a macOS boot volume is dead with macOS 12.4 (definitely for later versions of macOS). The developer of CCC has stated that the best that can happen now with the signed & sealed system volume is to clone your data volume and restore it after you perform a clean install of the macOS system volume. When using CCC to clone a macOS 11.x+ boot drive you will need to right-click or Control-click on the destination item in CCC and select "Legacy" to make the clone bootable, otherwise only the data is transferred (I'm not sure this still works with macOS 12.4).
These macOS cloning apps do not clone the empty sectors as these apps are basically gloried file copy apps with special abilities, although when using these apps to clone a macOS 11.x+ system these days, these apps must utilize the macOS ASR utility which is basically transferring an APFS snapshot which may be actually be doing more of an actual clone of the file system.
https://bombich.com/kb/ccc6/cloning-macos-system-volumes-apple-software-restore
If you wanted to clone the entire physical layout of a drive sector by sector, then you would need to use a special utility to do so, but this won't work correctly with later versions of macOS nor does this option work when transferring to a different size drive (impossible to go smaller, but going to a larger drive leaves wasted space that can be difficult to merge). While macOS has a built-in command line utility "dd" which does this low level sector by sector clone, it is both dangerous/risky to use plus it does not show the progress or allow for resuming an interrupted clone. The best free open source command line utility which takes "dd" and makes it better is GNU ddrescue which is used by many data recovery specialists since it adds these features and also has the ability to ignore bad sectors on a drive. Both of these utilities are dangerous/risky to use because it is very easy to select the incorrect destination which can overwrite important data. "dd" has been know as "disk detroyer" and "data destroyer".
You should definitely read some of the CCC developer's articles regarding cloning macOS boot volumes with Monterey and future releases of macOS:
https://bombich.com/kb/ccc6/macos-monterey-known-issues
https://bombich.com/kb/ccc6/frequently-asked-questions-about-ccc-and-macos-11