I've bought two flush caps for my Iron so far and neither fit.
There is a metal tube sticking up in the fill hole that blocks the gas cap from screwing in all the way.
Can I trim that tube down so the gas cap will screw in all the way?

 

Your metal tube looks weird. Is that a screw at the top of the tube? Mine does not have the screw and is an open hole.

Try removing the screw and see if the added clearance is enough for you.

 

it's not a screw, it's a rubber plug that is pushed into the tube.
What year is yours?
I bought mine new and it came this way

 

These Chinese made flush caps fit after a bit of DIY, I did mine in the lathe. You need to turn or grind a bit of the inner part diameter , it is not much so you can use a dremel if you
have no acces to a lathe.

Here is mine fitted on a 2017 Iron , after the work was done.

 

I just took 2 extra pictures for you from my gastank to show you it's exactly the same as yours and a closeup from the inside of the gascap that I altered. This gascap I use for more
then a year now, no problem at all.

 

You have to remove the parts that are yellow marked.

 

Odd, my son's '17 Iron doesn't have that plug in the vent tube, and neither does my '17 SuperLow.

Something to do with California emissions maybe? I know on my bike once I filled it up sitting straight up and when I rolled it out onto the drive and put it on the sidestand I had a small puddle of gas on the driveway. It was dripping out of the vent hose, apparently California doesn't want that to happen. Wonder how a California tank vents if over filled?

 

I've never seen a vent tube stopped up. What good is a vent tube with a stopper in it.

 

My 17 Iron has the stopper in the vent tube, my son's doesn't.

I put an H-D flush gas cap on mine.

 

I wonder if HD puts the plug in the vent tube to prevent anything getting in the tube during manufacturing/assembly, and is supposed to be removed when the bike is fully assembled? But it doesn't explain how the bike would run for more than a few minutes with no vent since it would start to form a vacuum in the tank.