I just like to document as accurately as I can, what is being grown. Rootstock affects flavor/vigor/ etcetera, right?
That and i was tempted to let the rootstock stem grow controlled so I can graft others onto it. Bad idea?
Mango, avocado, stone fruit and citrus rootstock could be important. Loquat, not so much.
Yes, bad idea to keep that shoot below the graft. Cut it off. If you want to make a franken tree, then graft onto the tree's branches or better yet, just plant seeds and graft away.