anywhere in the water flowpath you place that media, it will pick up bacteria.
side note: no extra surface area is required in reefing beyond live rocks in the display, all else is merely extra surface area that would run your reef the same even if you didn't use it. in other words: it doesn't matter if surfaces beyond common rocks in the display are cycled/pick up bacteria/or not, because those surfaces aren't needed. reefs don't run low on surface area, requiring extra or more to be packed in a sump, or filter. that's merely training from freshwater keeping everyone assumes applies to reefing, but doesnt.
whether or not you use extra matrix surface area absolutely does not help, nor harm, your reef tank. it's neutral impact/not needed at all in fact. no reef employing matrix is safer, more stable, or better off than one not using it.