And for most users that security warning is as good as a cryptographic lockdown anyways.
On the other hand, I find it ironic how a lot of "security professionals" will complain constantly about users accepting security warnings with no thought anyway (and they usually use this argument to justify their increasingly authoritarian measures of controlling them.)
Apple does the same thing with Notarization and Gatekeeper on macOS. If they choose to revoke your signing certificate, Gatekeeper will prevent your software from running on macOS.
That means if you do, say or compete with something that Microsoft or Apple doesn't like, they can prevent your apps from running on their platforms.
A generic answer to your question is that the software was signed by whoever compiled or distributed the software, which can include your own machine. Your own key is in your trust store or your app distribution method put their key in your trust store. Both macOS and Windows will treat software compiled on the same system it is run on as blessed to run without strict signing checks.
On macOS, ad-hoc certificates can be used, but the OS will treat those binaries as if they're radioactive. If you compiled code on macOS, the system will treat that software specially on that specific system and allow you to run it[1]. On Windows, certificates can be added to trust stores. Chocolately, for example, has their own signing certificate for all of the compiled open source software they have in their repositories, so Windows allows their software to run.
The biggest issue is what comes with software distribution itself, where your code isn't blessed by default by the system it was compiled on, or doesn't have signing certificates in the users' trust stores, and Gatekeeper and Windows Defender go out of their way to stop your users from running software with signing certificates they don't like.
Every browser I know uses the Mark of the Web to tell Windows that a file came from the internet. You'll have to store the file on a FAT32/exFAT drive to get rid of it. If a file comes from the internet, smart screen kicks in.
When a file is unsigned, smartscreen essentially prevents you from running the file. You can work around it, but I had to look up a tutorial myself.
If the file is signed, metadata will be extracted and submitted to Microsoft. If that fails or the exact binary hasn't been run on a certain amount of computers, smart screen will show a big scary warning despite your $500 a year digital signing certificate. This is something developers just have to deal with every time they update their applications, but most people won't be the first x to download the executable and applications using auto updaters download updated in the background can the necessary flags to work around smartscreen.
The restrictions are there, but they're not there for (most) development environments and for most users of popular software.
This is true and annoying, but only with regular certificates. The more expensive EV certificates bypass this “well known” check.
I learned long ago, and keep it clearly in my mind, that what AV considers "malware" and what the user considers malware are not entirely the same.
and if clearly false could be used in court.
I do wonder if Windows becoming adware, but then the built-in antimalware detecting possible "competitors'" adware and removing it, could be challenged in court as anticompetitive behaviour.
You, personally, can turn off Windows Defender, but your users probably have no idea why the app they're trying to run doesn't work when they double click it. They're also probably shown multiple scary warnings that discourage them from using the app and trick them into thinking it's broken or malicious.
It's a hurdle just to convince users such an app isn't malware, and then it's an entirely other hurdle to help them actually run the software by bypassing Defender.
Are there examples of Microsoft actually doing that?
Ability to prevent known malware from being run in the majority of PCs after detection seems like a useful feature from the Internet health point of view.
The huge difference is that's only a warning, and not a cryptographically locked-down system unlike Apple's.