I can confirm other's suspicions that the loops on the kilt are indeed for hanging. If you fold the kilt as though it were being worn (aprons overlapping, etc), and then fold it again in half, along a vertical line, with the pleats to the outside, the two loops should come together. Those can then be used to hang the kilt from a peg or something similar. As has been pointed out, though, this is not for long-term storage.

As for the join on the inside, this is actually quite common on most kilts these days, the reason being that most all tartan is 54" wide (or more), meaning you can make an 8 yard kilt from a 4 yard length of cloth (or a 4 yard kilt from a 2 yard length, etc.).

If I am a kiltmaker who has an order for a kilt in the MacGregor tartan (just to pull a random example), I'm going to order the 4 yard length I need to make the 8 yard kilt. It doesn't make sense for me to order an 8 yard length when I only need half the cloth, and to then sit on the other half of it waiting for another order in the same tartan. If I were only offering a few tartans that would be a small matter, but when you consider the thousands of tartans available, it doesn't make sense to order any more cloth than you need for the one kilt.

The key thing about the join is that it should a) be hidden; b) be securely stitched; and c) preserve the sett of the tartan.

So long as those three conditions are met, I wouldn't personally lose too much sleep if the lines of the tartan go a bit wonky, so long as it doesn't visibly affect the hang of the pleats.