I've never heard of a pomegranate being propagated by grafting. Cuttings are stuck into the ground and rooted for new trees. Cut away two of the trucks and volá -- you're set with a single trunk tree. Don't worry about bare spots. Poms are very forgiving, and will be sprouting new branches all over. In fact you'll need to remove many of the new sprouts to maintain the single trunk form.

The wood is very pliable and will not make a good tree. I have seen 50 year old pomms' that still could not support a tree structure. You might be able to espalier it or train it to a very sturdy stake but it will not prune up for a tree well at all.

Every pom I've ever seen has been, more or less, a large, multi-stemmed shrub.
I've had 'em at my parents' home for 40+ years and never pruned, other than to remove a broken branch here and there.

Years ago I bought a Wonderful Pom that had been trained as a tree. It has never been a good tree and I wish it had not been trained up. The trunk is still spindly after 15 years and it suckers heavily from the ground. Al