They started as separate bills in the House with a final step of merging them into one before sending off to the Senate, as I understand it
Even if they were technically separate at one point, the discussion leading up to and throughout was about them as one. The Senate passed a bigger bill that also included border funding months ago. That was rejected by the House without consideration or negotiation, because reasons...
Regarding "fairness" of bundling, I agree with others this is the wrong framing. Democracy and politics is about giving and taking to get something not perfect through a messy system full of competing interests.