Yes exactly, except for pull requests, in a pull request you will see only the issues added on the code that has been added in the pull request.
But when looking at your main branch, you will see both the issues on old code and on new code. For example on that screenshot, you can see on top of the yellow background the issues for the new code (which is a 30 days new code period in this case). And on the left, on top of the white/blue background, are the issues on the overall code (old and new):
And here you can see that the quality gate is passing (green) even though there is an E rating on the security hotspots on the overall code, and this is because our default quality gate conditions are based only on the new code, but you could customize it.