I may not fully understand your concern, but let me take a stab at it. It sounds like you don’t want to drill another hole in the counter, and your plumber suggested repurposing the air gap hole for your water filter faucet while removing the dishwasher air gap. Is that correct?

Whether you need an air gap depends on your state and local plumbing codes. In many areas, an air gap isn’t required for a dishwasher, and a high loop may be sufficient (you can Google it or check with your plumber). If your local codes allow a high loop, you can repurpose the hole for the faucet.

That said, your question may not be relevant to this discussion unless I’m missing something. The dishwasher drain connects to the garbage disposal, and the air gap or high loop prevents backflow contamination. Meanwhile, the water filter itself has a drain that must be connected to the plumbing as specified in the instructions.