Issue was caused by file output node actually, The thing here is, compositor output does have fixed resolution and we could predict how to map coordinates for border and cropping in that case. But viewers and file output nodes are currently totally depending on an input resolution. Could not see how border could be applied reliably in this cases. Disabling border option for file output node, so now it shall behave the same way as it was before. Discovered issues when using cropping to render border, namely there's an offset in viewer nodes and previews, but this is separate issue i guess (file output seems to work fine). Will revisit this issue in next days.