Hi Nick,
Sorry you didn't get a reply, hopefully you get a notification.
The reason your branches look like they've been grafted on is because they are long and thin. This can be just the natural way your tree has put out branches. Just because the base is compact, your tree can still throw out long, thin branches.
One of the aims of bonsai is to keep things compact in order to look like a miniature version of a tree. One of the things that gets talked about is ratios; the main idea is keeping everything in proportion. So, if you have long branches and a squat base, then things look out of proportion.
To get your branches back into proportion, we usually cut branches back. By cutting branches back, the tree responds by putting out new growth and the branches get thicker. You also get shorter branches, which again, make them look more in proportion. In theory you get shorter branches, thicker branches, more compact branches, smaller leaves and closer leaves resembling a canopy.
A couple of things to mention: All of the above takes time, lots of time and patience. It also comes with risk, but so does looking after any living thing.
I highly encourage you to check out Adamaskwhy blog
https://adamaskwhy.com/ Adam's main focus is Ficus and my love of Ficus and many of the things I've learnt have come from his blog.
It's also worth knowing that you should have had a lot more growth over 13 years. Trees that have been put in the smallest possible pot will have their growth restricted. If you want to progress this tree further look into the purpose of fertiliser and regular (not frequent) re-potting.
Good luck
