You can't add effects to a transpatent layer, because there's nothing to see that would be affected. It wouldn't help much to add effects to an adjustment layer, because they affect everything below them. Just re-think how you apply the various effects to the one layer. Or duplicate the layer, add effects to one, leave the other alone, and mess with blend modes & opacity.
The very first thing I would try is a duplicate of your footage player with the overlay blend mode enabled. This will darken anything below 50% gray and light and everything above. Apply your strobe effect to that. If you do not like that result than apply your strobe effect to a black solid with the blend mode sent to add or screen.
Thanks very much to both for your help -- I'll try that out Rick, and bear in mind what you said Dave for the future!
Thanks very much for your help.