You absolutely have to pay for an extended validation code signing certificate for Windows 10 Smartscreen to allow your installer to run.

That's not true. Binaries can acquire a positive reputation by being commonly downloaded. However paying for an EV certificate (or getting windows logo certification) is the only way to bypass the warning with no reputation.

What new developer already has a reputation score?

You absolutely have to pay for an extended validation code signing certificate, or your installer will be blocked by default.

Third parties charge more for that code signing certificate than Apple does for a developer account.

No new developer already has a reputation score. Why should they? Is there something unfair about warning users that uncommonly downloaded software is more likely to contain malware?

If anything, the problem is that even software with an EV certificate should be subject to the warning (like how SmartScreen worked in the past).

The entire point of Gatekeeper and SmartScreen is to only warn users about unsigned software that could install a trojan horse.

If you check to see if the developer's signing certificate has been revoked before running their software, you can be reasonably sure that doing so is safe.

Apple's developer program is cheaper than the extended validation code signing certificate you need to develop and sign software use on Windows without running into a block from SmartScreen.

No, that might be the point of Gatekeeper but the point of SmartScreen is to warn you when you are running uncommonly downloaded software. You might be right that it is cheaper to buy a guaranteed exception for Gatekeeper than it is to buy a guaranteed exception for SmartScreen though, but I don't think that is relevant when you don't really need an exception for SmartScreen at all.

No, stopping uncommonly downloaded software from running is Microsoft's way to force new developers to use their app store, since software distributed from there is exempt from that limitation.

Apple's developer program is not only cheaper, it allows for functional code signing that completely sidesteps their app store.

SmartScreen existed prior to Microsoft's app store though.

I am not sure what you mean regarding your point about sidestepping Apple's app store. Code signing can obviously be done on either platform without any app stores.

No, SmartScreen blocks software that doesn't have a high enough "reputation score" even if it is signed. The only way around that particular restriction is to distribute your app through Microsoft's app store.

Gatekeeper has no such caveat.