Most themes don't modify the admin panel, and that code is in the default order_form.tpl file, so I don't think this is a Journal issue.
The order editor in OpenCart is complex, because it uses the API to call front-end functions to get the order information, and rebuild the order as you edit it. It can be hard to follow all the paths, because it's not the usual "look in the controller file" process. You may need to hire an expert if you can't figure out the process and get the bug fixed (or can't find a fix for it in the forums).
For your questions, here is some clarification:
1. All variables are defined in the related controller file. In this case, that would be /admin/controller/sale/order.php. You'd look for $data['order_products']
2. The products with different options getting combined would be a bug in my estimation. I don't know if this occurs in a default 2.3 installation, but if it does, you should look in that bug topic to see if there's a fix for this. I would think someone would have reported it if it's a bug in the default version. If you want to try fixing it yourself, you'd probably need to look at the front-end getProducts() function. Based on the ajax code that calls it, the file path should be this: /catalog/controller/api/cart.php
If you can't find a fix, I do have an Edit Order Line Items
extension that can edit orders in a process completely separate from the built-in order editor. It won't have the issue of combining products with the same product_id, because it uses an independent process to get the order information and edit the order (not using the OpenCart API).
Feel free to take a look at the screenshots and demo site, and if you're interested let me know at www.getclearthinking.com/contact
if you have any further questions.