You can fix this pretty easily if you use a browser extension like Stylebot to customize your page styling - it's great when something just annoys you aesthetically.
Here's my first pass at a correction that seems to work with the main pages, although I'm sure I'm missing something somewhere:
.home-page .killer-logo { top: 40px; overflow: visible; }
.killer-logo { top: 82px; overflow: visible; }
.home-page .wide-hero, .issue-page .wide-hero { padding-top: 136px; }
.wide-hero { padding-top: 98px; }
.global-footer { padding-bottom: 100px; }
.deadly-subtitle { bottom: 10px; height: 60px; }
.global-footer .inline-items { margin-bottom: 2px; }
.main-wrapper.stacker:first-of-type { margin-top: 198px; }
.single-column-display, .two-column-display, .multi-column-display { margin-top: 198px; }