When I had this problem it was another female coming to my porch. She looked pregnant or with kittens b/c her belly was big. She was going after my 2 ferals Ace and William and chasing them off the porch- lots of screeching was happening a lot!
I did trap her and took her to be spayed. She DID have 2 newborn kittens and that was why she was being so aggressive. I found homes for the kits- they survived thank God. It was not a fun situation
I really feel for you, Barb, I felt so protective toward my kitties, and I was really mad at this other kitty even tho I knew she was just surviving.
After this little girl was released she did not come back to my porch. I have seen her once since then but she doesn't want anything to do with my house.
I still feel bad that I could not also find a comfy spot for her, but as with your situation, they did not want to all be one big happy family. My feral female hated her. I even put a kitty house out for her on the other side of my house, but no luck. Plus they all considered the entire outside perimeter of my house to be their territory, so there was only room for Ace/William or the other kitty.
So, you might try trapping this guy, but I know you have the problem of getting the other kits instead. Plus I'm not sure it would make your guy go away. It sounds like that shelter is something he really loves, along with your house and the food.
As the other poster suggests, you could do another makeshift shelter. If it were me, I would get 2 outdoor cat heating pads and some fleeces to make a donut around the pads; and put them under another solar pool cover, making a tent between two deck chairs, putting bricks around the floor, and leaving a little space open for the kits to go in. It is possible the Tom will prefer this to the house, even. You could put the bedding from the house he is in right now, into the new space for him. My feral male prefers to sleep on the floor of his winter house area- quick escape.
I know your kitties already have the space under your deck- the only other thing I suggest is putting the second solar cover on top of the deck, therefore sealing it better, and putting the heating pads underneath so it helps to enclose that space better and they will be warmer under there.