That's what we found out:
ReportViewer has some tolerance when two tablix overlap, the second tablix is moved down, just below of the first. That's how it would have been intended by design. So we never had an issue with the buggy definition. Rendering it to PDF on the other side is absolute strict and tablix will overlap in output. The only solution was to go throw our files and correct them, so that they are shown as before in Report Viewer but are also rendered correct.
There is no special configuration for printing view or layout.