Rules in deep folders run after rules in the root.
It's possible that a root rule matches a request that should not do so.
I find it less complicated to have all the rules in the root.
There's major problems if a deep htaccess external redirect runs after a root htaccess internal rewrite.
Make sure you comment your code for when you look at it a long time in the future.
Let's see the new code, as there's a couple of minor issues to finish off.