OP I know you have good intentions but you're really way off mark.
Your GF and Tom's Father Besides logistics, the only people talking to each other about Tom and his parenting should be your GF and her ex-husband. They are his biological parents and if Brandy or you get involved, it will only make things more messy than they already are. I am also very concerned that neither of you seem to understand that it was not appropriate for your GF to take Tom over to 'discuss' his feelings with his step mother. Your GF should have told Tom that she will talk to his father about this and for him to not worry about it anymore. I get she was trying to solve the situation but asking a 12 year old to be responsible for communicating his feelings to another authority figure in his life is putting too much responsibility on him. Tom would also be picking up all the other dynamics going on between his Mum and Brandy, I'm not surprised he's wetting his bed, poor kid, I feel sick just thinking about it. If talking to her ex hasn't worked before, keep trying or go back to court. The answer is not to put it on the kid.
Calling CPS? Don't. Although I don't think much of Brandy's parenting style, to impose societal expectations of gender roles is hardly a cause for removal of children. CPS is there to protect children when there is genuine concern for their safety and welfare. It is not a weapon to be used against either parent. As mentioned by others here, document and go back to the Family Court. By the way, CPS would certainly think your GF made a serious error in judgement if they heard about the above story.
Fraud Collecting food stamps when you're not entitled to them is not right, it's fraud. You really need to reassess your moral compass. Fraud affects all tax payers, it's a crime and it doesn't set a good example for her children. If your family was starving then I would get it, but you're not. She has the luxury of studying while other single Mums are busting their guts working 2 or 3 jobs to support their children. They are her children, not mine, I don't want to support them and I certainly don't want to support her studies. Your sense of entitlement because she's trying to break the poverty cycle astounds me. She has your income and child support and only as the kids half the time? She's in a better place than most single mothers I know.
Finally you call Tom's father a POS. Sorry but I had a hard time finding anything in your post to suggest as such. Brandy is a concern, but so is your girlfriend. Also, you're not even their step father, you're a live in BF. I'm also pretty sure if you harbour these strong emotions about their biological father, a man that they love, they can pick up on this. Children are not dumb and they pick up on non-verbals and vibes.
I implore you to sit down with your GF and start putting her children first.