I'm on a Realm, and yeah the hopper minecart is going under every block the items are on. I tried moving the rail system a level up so it would be closer but that didn't work either. I built this exact farm in a realm like a month ago and it worked normally so I don't know what's going on here.
The hopper minecart is pictured below - I meant I moved the whole thing a block up but then it was rubbing against the magma blocks and wasn't running. The 3x3 magma area in the second picture is where the items are supposed to be picked up. I can't replace it with slaps because the creepers wouldn't die that way.