It's possible to make a polyobject door that doesn't block above or below itself. What you have to do is make the holding sector as low and high as the sector the door will actually be in. Then create polyobject inside as usual (but skip the textures for now). Then, create a 3D floor in the entirety of the holding sector at the same height and tallness you want your door to be, you can leave the textures blank. Now you can set the middle textures for your door on the polyobject's lines and raise or lower them until they're INSIDE the 3D floor (the top and bottom floors of the 3D floor should line up with the doors textures). You don't need to set any special flags for them, as the 3D floor itself will define the collision heights. Example map included to help illustrate the above.
Disclaimer: You can just set the polyobject's lines to "walkable middle texture" and forgo the 3D floor part altogether, however it won't block hitscan weapons unless you set the appropriate flag to do so, and even then it'll block those weapons above and below the door as well.
There's also a problem with the 3D door in my example map where it won't reverse course when moving and it collides with a player, causing them to get stuck underneath. I'm not sure if this can be fixed, so probably the above implementation shouldn't be used for doors where it's possible for the player to collide with it when it's moving.
You do not have the required permissions to view the files attached to this post.