Well what I mean is that style preferences in IB2.php (like definitions for row colours) are CSS dependant, so with a custom skin for the forums they may need to be changed. This means that when you upgrade the forum code, ib2.php is overwritten and any customizations you have are then lost.
Things like "$Style['catcolumn'] = "row1";" may be user defined/customised you see.
To me it'd seem to be a huge advantage to have these defined in a separate user file that's not code related so that they aren't overwritten in an upgrade.
It's just a suggestion after all