I've found that you shouldn't have a great deal of the marinade left over to think about reducing into a glaze. The thought is that no matter how much you use in the container or bag you put the products into, the item you are marinating is going to only absorb so much. There's no sense to use a gallon when a cup would suffice. I have always made marinades in bulk and portioned them for the appropraite size use. Jayme is spot on about everything including the saving some and using it for the glaze.
As far as the bacterium and it's toxins are concerned..... Aren't most marinades acidic by nature? I have always believed because of the acidity it helped to curtail any or almost all rapid bacterial growth. It's also been my belief that it doesn't usually go bad unless it sits around in the cooler/refrig for weeks after use or until you have introduced so much of the meats natural juices (blood from using the marinade too many times) that the marinade looses it's acidic properties and then can become a breeding ground for this bacterium. If toxins were going to be present wouldn't the initial use be affected and then wouldn't that affect the safety of the meat in it. Hopefully before anything could happen that makes the food unsafe, the user would realize the marinade was useless and already discarded it. The "3 strikes theory" or a week SL in total works well for this.
So IMHPO use less marinade in the process and reserve more of the unused for reducing