I don't really have a problem with transports taking a slot. Also, your numbers for troop size don't match up with how I'm using them. I've been using 'troop sink' APs for awhile and am simply doing the same thing with portal cities. Basically, if you have enough warehouses, you can sacrifice a single AP/City and significantly overcommit your resource creation. When you want to use the portal, you need to make sure you send troops to the troop sink city/ap with enough gold/food that they can port to the warzone and still move around. You do need to be careful and use the portal right away when they enter the city because your food/gold will disappear quickly.
As it is, so far I've sent 1.5 million troops, via five 300k armies, through the portal in one city. I still have enough overcommit space available to send plenty more. You can't use that city for troop generation, of course, but that's no biggie cause all of your other Cities/APs are free of the upkeep from those troops so you can build more with them.