Yes, that fee includes the ability to sign iOS apps for local distribution and submit them to the App Store, where apple will sign them. On macOS, it also allows code signing for general distribution like Windows has, as well as App Store submissions.

I think the issue most people have with the price is that on iOS there's way more limits on running locally without a cert (7 days max), but for someone who is a practicing developer it's really a pretty low cost. If only it came with a mac to develop on...

It's also a part of Microsoft Store development fees (similarly $99 last I checked), if you release through the Store all code signing is handled through the Store.