If you're using the MR Baking options you can do it. You can go in to the directory that has this GUI and change a few lines to get it to ignore the "miGetRootDir;" command and change it with your own.
I went to try and find that script that makes the UI for that and it can't be found. You can rebuild your own UI to inject your own options, and call to bake when ready.
I also ran into this a while back, it took me bloody ages to work out that that's what the "Image Prefix" would work for, seems like a horrible UI decision, not consistent or clear at all.
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Found the file I think: scripts\others\mrBake.mel
I also ran into this a while back, it took me bloody ages to work out that that's what the "Image Prefix" would work for, seems like a horrible UI decision, not consistent or clear at all.