I can't speak for your own brain, but I read a translation once (don't remember what) where they'd mirrored it so it could be read left to right and it absolutely threw my brain for a loop
You tend to finish the right to left line to the end of the page before moving down any. So if 2 panels are in the same "line" like 2 and 3 are, then you finish out that line before moving down. In a case where one panel is larger and spans multiple lines it'll generally be laid out to belong to it's lowest line if it's on the left side of the page, or the highest line on the right side of the page. So since 12 covers both the line with 9, and the one with 10 and 11 on it you'll generally read it as belonging to that lower line and it'll be 12.
I really am new to manga, but what I have noticed so far is that there are subtle flow queues in the art itself. For example, there might be a very thin line between those three cell and a thicker border between them and the larger cell to the left.
Kind of, yeah. Though if a larger panel is on the right rather than the left you consider the top of the panel rather than the bottom. So like if you swapped 12 with the 9, 10, 11 cluster it would just be 12, 9, 10, 11.
I like that when I line them up on a shelf in numerical order, all the pages are lined up in order as well, with the end of one book touching the start of the next.
If it's a Western-style book, yes that is so! And by ascending numerical order, I mean number 1 on the left side. When you put English language Book One on the shelf spine facing out, its cover gets turned to the right side (unless it is upside-down!), touching back cover of Book Two. But Manga will have front cover of Book One snug against the left side of the bookshelf, and its back cover touches front cover of Book Two. You should go try it with your books, just to see it happen. Feels good.
Fun fact, it used to be right to left (1 letter each and line break in vertical writing, then right to left columns) before they adapted left to right western writings.
They're mostly gone by now but still some old places keep the order. For example, trad confectionary place named とらや toraya have their shop curtan reads inverse やらと yarato)
Ink runs when dragged over by a right handed writer moving left. Some systems are objectively better for some reasons, and while accepting all of them as uniquely useful is fine, it’s certainly not an answer that sates my curiosity
Japanese was written vertically, so characters are ordered from top to bottom while it is the lines which are separated from left to right. The slow leftward advancement allows a person writing on a scroll to write with their right hand while unrolling the scroll gradually with their left. In modern times you can write Japanese horizontally, but in that case you usually write from left to right. Characters written horizontally from right to left is only done in exceptional cases.
I just realized that top-to-bottom also solves the problem with smearing discussed in another comment. Your hand is moving down, away from the fresh characters. By the time you move over to the next line, the top is already dried. (Especially with the time it takes to fill a line with kanji, which are denser than Latin script.)
I don't know if there is an advantage or disadvantage. There are other writing directions as well. Like boustrophedon, which starts in one direction, and then when you get to the end of the line the next line goes the other direction. This sounds like a better way to write to me!
Egyptian hieroglyphs can be written either RTL or LTR, you tell because the animals and humans in the script face the beginning of the line.
Basically the priority is to make as many unbroken right to left lines across the whole page as possible. You don't generally move down unless you've reached the leftmost edge of the page. Notice how here if I draw lines across the panels to show the path my eyes take and read 12 before 10-11 my reading line is going to run back into the line I made already? So you read 9 and go to the next line, considering 12 to be part of that lower line so that your reading lines don't intersect.