The header changed from using position: fixed to position: sticky (https://github.com/discourse/discourse/commit/da5841de0b2b60ceaa2f2602d7231e7393a74e66) - this is one of the updates we’ve been able to make due to dropping IE11 support.
The change improves some small issues we’ve had with the header since Discourse has existed… what it means functionally is that instead of being in a fixed position (and unrelated to the position of other elements on the page), the header is now part of the natural flow of elements on the page… which is why the main outlet padding and margin are no longer needed.
When the change was initially made there was some extra padding on mobile in the default CSS, but that was fixed a day or two later… I’d guess you updated on the day between the initial change and the fix, if you update it again it should go away (you can alternatively add .mobile-view #main-outlet { padding-top: 0.25em; } if you don’t want to update again).
Your fix with .d-header-wrap seems sustainable to me.