Is it possible the answer you're looking for is just to nest basically everything in your dashboard downstream from the Checkboxes? This is one of the ways in which the framework is pretty unintuitive, but the modules do now know or care what layoutPanel they're in. So you can do what you like.
for instance this pseudo-xml would result in a Checkboxes module at the top whose token can be used in any of the other searches on the page
Search layoutPanel="mainSearchControls" autoRun="True"
Checkboxes
Search layoutPanel=panel_row1_col1
Table
Search layoutPanel=panel_row2_col1
ValueSetter
JSChart
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