I'm a little hesistant to call this a bug, but it is an inconsistency and (at the minor cost of having to render two more divs sometimes) having the markup consistent would make theming easier in some cases. I know this because I had an idea for presentation, and was trying it out, and... :D
The thing is, in both templates you are usually going to want the same presentation for categories (BoardIndex) and child boards (MessageIndex) but the .boardindex_table class is effectively doing two different jobs in the two templates, and in MessageIndex does not have the other two divs to back it up. This can make non-standard presentation awkward.
<div id="content_section"> <!-- Global wrapper div -->
<div id="main_content_section"> <!-- Global wrapper div -->
<div id="boardindex_table" class="boardindex_table"> <!-- Consistent class to here -->
<div class="main_container"> <!-- Wrapper for all of category -->
<div class="cat_bar " id="category_10"> <!-- Generic category header -->
<h3 class="catbg"></h3>
</div>
<div id="category_10_boards"> <!-- Wrapper for all boards in category -->
<div id="board_31" class="up_contain "> <!-- Generic board -->
<div id="content_section"> <!-- Global wrapper div -->
<div id="main_content_section"> <!-- Global wrapper div -->
<div id="board_20_childboards" class="boardindex_table"> <!-- Consistent class to here -->
<!-- NO wrapper for all of category -->
<div class="cat_bar"> <!-- Generic category header -->
<h3 class="catbg"></h3>
</div>
<!-- NO wrapper for all boards in category -->
<div id="board_132" class="up_contain "> <!-- Generic board -->
The logical way of dealing with it would seem to be this:
<div id="content_section"> <!-- Global wrapper div -->
<div id="main_content_section"> <!-- Global wrapper div -->
<div id="boardindex_table" class="boardindex_table"> <!-- Consistent class to here -->
<div class="main_container"> <!-- Wrapper for all of category -->
<div class="cat_bar " id="category_10"> <!-- Generic category header -->
<h3 class="catbg"></h3>
</div>
<div id="category_10_boards" class="category_boards"> <!-- NEW class added -->
<div id="board_31" class="up_contain "> <!-- Generic board -->
<div id="content_section"> <!-- Global wrapper div -->
<div id="main_content_section"> <!-- Global wrapper div -->
<div id="board_20_childboards" class="boardindex_table"> <!-- Consistent class to here -->
<div class="main_container"> <!-- NEW wrapper for all of category -->
<div class="cat_bar"> <!-- Generic category header -->
<h3 class="catbg"></h3>
</div>
<div class="category_boards"> <!-- NEW wrapper for all boards -->
<div id="board_132" class="up_contain "> <!-- Generic board -->
I can't see this causing any issues, and I can see it being useful sometimes. :)