It looks like that brown part on the bottom is the grafted fruit part. The thick branch is rootstock.

More opinions?

Aside from rootstock growth most all citrus only need to be pruned for the 3 D's. Dead, diseased,damaged. Sometimes you get an occasional water sprout which I think is what you have growing up the middle that usually needs to be dealt with.

Both my Meyer lemon trees turned into Cuban Shaddock trees the way your tree is changing. If you new how to graft I would t-Bud up higher on that sucker but I don't and I should have cut it off.

If you could attach a closer-up picture of the branch and trunk junction, it would be helpful--but it does indeed appear to be rootstock. Can't tell for sure though.

Here is a closer-up shot of the general branch and trunk junction. I will post some other pictures below

This is a picture taken from the other angle... the largest branch that's closest in this photo is the one in question that has grown straight up and taller than the rest of them.

Finally, and here's what's confusing to me... this is a closeup picture of the suspected rootstock. But on this trunking 'rootstock', there is an offshoot quite a bit above the junction that is a fruit bearing branch. The rest of them though, no fruit at this point.

I believe you are safe. One of the main methods citrus grow is through water spouts that shoot above then branch out and fruit. As the older limbs bend out they loose productivity and may be discarded by the tree in favor of better newer better placed growth.

Yes, I think you just have a vigorous water sprout - which is scion and not rootstock, from what I can see. This is normal for citrus. It will eventually bear fruit. You can just cut it back to just below the lower 'bush' height it you wish. It should then branch out more densely. These are trees, after all! Looks like a very healthy plant.

Thank you very much everybody for the feedback! I will cut back the bottom portion once that fruit ripens, and go forward with hopefully a very healthy tree for years to come! Then it becomes a matter of keeping it under control for height since I still need to be able to bring it indoors and out.