I haven't read the bill yet though and can only assume the Senators writing the bill have considered your point. That said, you know what's said about government work.
Well, what you are talking about is the “black budget” funding for the DOD, but despite its name, it is not actually used to fund programs that are illegal, only highly secret programs. The very nature of illegal programs means you must avoid Congressional oversight, and to do that, the most important thing is not to fund them with the Congressional purse.
Not that it never happens that a line item is “misdirected” to an illegal program as a lazy shortcut to obtaining outside financing (or secret internal departmental financing, which does exist outside of Congressional oversight). But even in such a case, the line item would say something other than “Illegal UFO Retrieval Operation: $68 million”, and therefore it wouldn’t be an apparent violation of whatever law they pass. My point is that some Congressmen sitting in Washington DC will never be able to use a pen to stop a program they don’t know about, and a truly illegal program is one they will never have the opportunity to know about, unless some really screws up.