The Master Keyer's pretty sweet. You know this, and I know this. It has one glaring issue as I see it, and that is the inability to input a gmask or axillary matte. It handles foreground/background integration very well, but it's rather rare that said foreground is without tracking markers and other crap that needs to get masked out. Only you can't mask it out because there's no gmask input so you're totally effed!
There's a simple fix.
Make your cleanup mask and comp the average color of your chroma-key screen (i usually just use a CC to get the RGB value or pick if off the little proxy in Batch) through that matte over your key-in footage. I usually do it over the foreground layer as well, but should you have a graded foreground and a flat key-in, just comp the graded version of that same blue.
Now, when you run the MK you'll get all that blue removed automatically and get to use the sweet foreground/background tools. I used this trick to get great soft edges off a completely out of focus dude yesterday.