You wrote about how the installers that are higher in the order overwrite the files of the lower order installers. The confusing thing is that from my subjective perspective things with a higher priority are on top and a lower number indicates a higher order. Just think of the Olympics: the guy on the first place, not the on the third place gets the gold medal, right? After I saw the numbers (1,2,3. etc.) below the "Order" column I knew what was my fault, but before that I was quite confused. Maybe you can add a note concerning this. Or my logic is just awkward.
:) No your logic is fine, I think most people have the same problem and get it upside down initially, in my case when getting to grips with it I thought I had it upside down, reversed the order of everything, then realised the order I had was correct in the first place so had to reverse my ordering again (See Footnote *).
And... the reason that particular aspect was left out of the guide is because the order can be inverted with Wrye Bash Order column, so that highest is actually higher up on your screen as opposed to being at the bottom of your screen. So left it up to the user - But I do give hints to solve this, by mentioning the conflicts tab. If you have an installer selected which has files which conflict with files from another installer, then the conflicting files will be labelled as lower or higher and from which installer they come from. With that information it then becomes easy to determine which installer/files are actually regarded as higher by Wrye Bash and will end up in the game.
Personally I prefer Highest to be visually at the bottom of the screen (installing last and overwriting anything before it). The reason for that is because if you look at a complex installer and its sub-packages, which adopts a numbered folder approach (10 Core Files, 20 Alternate esp, 30 green textures, 30 blue textures etc) whereby the last of those selected wins, then it looks odd to me if you have the main list of installers upside down....
9 installer
8 installer
..10 core files
..20 bigger textures
7 installer
..10 core files
..20 alternate esp
6 installer
5 installer ....... etc is just logically and visually wrong to me. Whereas ...
5 installer
6 installer
7 installer
..10 core files
..20 alternate esp
8 installer
..10 core files
..20 bigger textures
9 installer ....... has a better flow
This ordering though can only be decided by the user to their taste really so ... left it as is with hints to solve/get used to it.
Footnote * - The thing that made me change my load order the first time was actually because I mis-understood how Wrye bash installs your installers if you do them all at once ...
I dont wish to confuse you further, but it does them backwards

- In my idea of Better flow above, installer 9's files are highest and end up in game overwriting files from installers lower in the list ( 1-8 ), however if none of those were installed, and you multi-select them all to install at once, Wrye Bash starts with installing installer 9, then installer 8, then installer 7 ... any conflicting files from installers 1-8 just get skipped so that highest is still respected.
When you see that happen for the first time you immediately think "Nooo, its installing the last one first so it will be overwritten by the others!", which is not the case - Confusing, but it does it that way because it is faster programmatically than doing it the way you think it should.
Edit: Last note - If your installers have NO conflicts with any other installer, install order does not matter because no files are going to be overwritten, they will all end up in the game.
The conflicts report for each installer is the key.