Im aware of two different approaches:
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replace the matrix/flag with a 2d list (list within a list). This is only senseful if the number of set flag is much lower than the possible “flags”.
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Add a “deny collision with” list to every body. But this implies some ugly object-object dependencies. But if Bullet uses IDs anyway one may use them to speficify the objects. But then one has to deal with the proper cleanup which will results mostlikely in a O(n^2) or a O(n*log n) algo.