Yeah, custom skins might be different but you can still add them relatively easily. I've installed on about 8 different skins so far, and 7 of them had those lines, but it still worked on the 1 that didn't, just needed to figure out which "div" element to add it to. Here are the first dozen lines from the Classic Blue catheader_expanded template (with this mod's edits already added):
<div class="borderwrap" style="display:{$data['div_fc']}" id="fc_{$data['id']}">
<div class="maintitlecollapse" style="{$data['divstyle']}">
<p class="expand"><a href="java script:togglecategory({$data['id']}, 0);"><{E_PLUS}></a></p>
<p><{CAT_IMG}> <a href="{$this->ipsclass->base_url}showforum={$data['id']}"><span style=" <if='$this->ipsclass->vars['cat_styles_on'] && in_array( $this->ipsclass->skin['_skincacheid'], explode(',', $this->ipsclass->vars['cat_styles_skins']) ) && $data['title_color']'>color:{$data['title_color']}</if>">{$data['name']}</span></a></p>
</div>
</div>
<div class="borderwrap" style="display:{$data['div_fo']}" id="fo_{$data['id']}">
<div class="maintitle" style="{$data['divstyle']}">
<p class="expand"><a href="java script:togglecategory({$data['id']}, 1);"><{E_MINUS}></a></p>
<p><{CAT_IMG}> <a href="{$this->ipsclass->base_url}showforum={$data['id']}"><span style=" <if='$this->ipsclass->vars['cat_styles_on'] && in_array( $this->ipsclass->skin['_skincacheid'], explode(',', $this->ipsclass->vars['cat_styles_skins']) ) && $data['title_color']'>color:{$data['title_color']}</if>">{$data['name']}</span></a></p>
</div>
You can see where the lines are from that and use that to deduce which lines need editing on whatever skin you are working with. Simply stated, the div element in which you would need to add style="{$data['divstyle']}" is likely going to be the line directly beneath the top <div>'s, the one that contain the style="display:{$data['div_fc']}" and style="display:{$data['div_fo']}".
Let me know if you can figure it out, or you can always post the template bit here and I'll point out which lines need the edits.
It might be a good idea to do a test run on either the classic blue or ip.boardpr skins just so you can get a feel for it and see it in action.