This is a very long question and I am unsure that I've grasped it all.
I have no clue why you are using a separate multilevel list for the appendices. You should only need one level in your main list for what I am seeing.
Your main level MultiLevel List seems to be only three levels.
How to number headings and figures in Appendixes in Microsoft Word by Shauna Kelly
The maximum number of heading levels in any list is 9.
Do you have some government regulation that is telling you to use 11 levels?
You do not seem to be tying the bulk of your levels to existing paragraph styles.
The following is from my boilerplate answer on numbering. I have it for a reason. This is the tried and true way to get numbering that works. Please read through it.
If you use automatic paragraph numbering or bullets read Shauna Kelly's directions on numbering and bullets. Start with How to create numbered headings or outline numbering in Word 2007 and Word 2010. For large documents you must follow these directions or you will lose your hair!
(Mac version: https://www.brandwares.com/bestpractices/2016/06/outline-numbering-in-word-for-os-x/). For styles attached this way, you also control the left indents through the Define New MultiLevel List dialog not the Ruler or the Modify Style dialog.
This may seem a bit convoluted at first, but it really is not. Just follow the steps. Shauna Kelly's instructions use the built-in heading styles, but you can use any existing paragraph styles including your custom styles. There are, however advantages to using the built-in heading styles when you create a Table of Contents. Here are some more advantages: Why Use Word's Built-In Heading Styles? by Shauna Kelly Note, you can modify these built-in styles to look exactly the way you want.
You want to do this even if what you want is a single-level list if you want the most control over your list.
If you want, I can provide links to videos demonstrating setting up numbering linked to styles.
The basic idea is that the numbering is set using the Define MultiLevel List dialog with each numbering level being attached to an existing paragraph style. Once you have this set up, you should not use the buttons for numbering in the Ribbon but rather apply the appropriate style for that level.
You can save a document with this as a template for future documents if you want so you will not need to do this every time.
Styles in a multilevel list, when properly set up, can be a part of a [Quick] Style Set or applied by a macro using the Organizer method.