Customize the main toolbar?

I don't think so, but I'm not 100% sure.

I'm not sure what you are trying to do but there are a lot of options for re-configuring the Explorer UI. (Though there may be a few features to be uncovered along the way)

See http://doc.bazaar.canonical.com/explorer/en/tutorials/customization.html

To completely take over the toolbar definitions save the following XML as a file called 'toolbars.xml' in your user BzrExplorer config directory. (On Windows XP this is something like C:\documents and settings\<user>\application data\bazaar\2.0\explorer).

<folder title="My Toolbars">
    <!--
    This file contains toolbar definitions, one per folder.
    Folder titles are used as follows:

    * toolset:prefix - all toolbars start with these actions
    * toolset:suffix - all toolbars end with these actions
    * toolset:sss - a set of items that can be included in toolbars
    * kind:kkk - the toolbar for locations with kind kkk
    * bbb - a toolbar called bbb

    Most toolbars are lists of actions, toolsets and separators.
    You may use custom tools and folders as well. See
    http://doc.bazaar.canonical.com/explorer/en/tutorials/customization.html
    for the list of available action and kind names.
    -->

    <folder title="toolset:prefix" existing="replace">
    </folder>
    <folder title="toolset:suffix" existing="replace">
        <!--
        <separator/>
        <action name="All_Commands" />
        <action name="Refresh" />
        -->
    </folder>
    <!-- static toolbars -->
    <folder title="classic" existing="replace">
        <!--
        <action name="Start" />
        <separator/>
        <action name="Add" />
        <action name="Diff" />
        <action name="Commit" />
        <separator/>
        <action name="Collaborate" />
        <action name="Explore" />
        <action name="Work" />
        -->
    </folder>
    <folder title="expanded" existing="replace">
        <!--
        <action name="Start" />
        <separator/>
        <action name="Add" />
        <action name="Diff" />
        <action name="Commit" />
        <separator/>
        <action name="Pull" />
        <action name="Merge" />
        <action name="Update" />
        <separator/>
        <action name="Push" />
        <action name="Send" />
        <separator/>
        <action name="Log" />
        <action name="Work" />
        -->
    </folder>
    <!-- kind specific toolbars -->
    <folder title="kind:welcome" existing="replace">
        <!--
        <action name="Help_Contents" />
        <separator/>
        <action name="System_Info" />
        -->
    </folder>
    <folder title="kind:repository" existing="replace">
        <!--
        <action name="Info" />
        -->
    </folder>
    <folder title="kind:virtual-repository" existing="replace">
        <!--
        <action name="Initialize" />
        -->
    </folder>
    <folder title="toolset:tree-common" existing="replace">
        <!--
        <action name="Add" />
        <action name="Diff" />
        <action name="Commit" />
        <separator/>
        <action name="Pull" />
        <action name="Merge" />
        <action name="Update" />
        -->
    </folder>
    <folder title="kind:checkout" existing="replace">
        <!--
        <toolset name="tree-common" />
        <separator/>
        <action name="Push" />
        <action name="Switch" />
        <action name="Log" />
        -->
    </folder>
    <folder title="kind:branch" existing="replace">
        <!--
        <separator/>
        <action name="Push" />
        <toolset name="tree-common" />
        <action name="Log" />
        -->
    </folder>
    <folder title="kind:bound-branch" existing="replace">
        <!--
        <toolset name="tree-common" />
        <separator/>
        <action name="Log" />
        -->
    </folder>

</folder>

Now you can configure what you want to appear by uncommenting the actions. If you uncomment everything then you will have the standard UI. To change the order in which the actions appear in the toolbar just change the order in which they are declared.

Note that there does appear to be a feature that means you cannot have a completely empty toolbar.