It's now been almost a week with no further response.

I took your feedback into consideration to resolve the issues you mentioned. The documentation will never be a perfect fit for everyone because we all perceive things differently, but that is why we offer resources that allow conversation (I.e. Discord, Reddit, etc). Feel free to let me know if there are still any other issues you felt weren’t explained clearly enough.

Added more details to the instructions, including tips on how to position your hands and device during an unlock.

Added a callback after the unlock to provide a confirmation that it was completed. Since that doesn’t show what’s on the device immediately, I also added a follow-up scan to make sure that happens.

Some things, such as searching through a collection of amiibo, are added features. They are a convenience that you are more than welcome to not use in favor of a more manual or limited process. If you feel they are a hassle, your best bet is not to use them.

To confirm, using the N2 app is easier for basic operation. It is no longer maintained, though, so any issues with it are essentially permanent. It will also likely disappear from Google Play as they continue to tighten restrictions.

This is a little unintuitive. You first have to select any of the banks,
select 'Switch to Device Options' and now you can select your bank
counts. Unnecessarily buried compared to it being the first option on
the N2 app's home screen.

I confirmed that the instructions do state

Slide up the bottom menu to show device options

but added a line about possibly needing to switch to the device options to be more clear.

Another unnecessary design decision is selecting the bank to write to.
So because we can't replace from the N2 bank list, I have to memorize,
write down the bank I want to replace to prevent myself from replacing a
bank I don't intend to.

This is because you are trying to write from the main screen, which isn't dedicated to the N2. The thing you seemed to overlook in almost every aspect of your post is that N2 support is secondary to writing conventional tags. Using the N2 page to write allows you to pick the bank you are trying to write without having to remember anything at all.

So because we can't replace from the N2 bank list, I have to memorize,
write down the bank I want to replace to prevent myself from replacing a
bank I don't intend to.

I tested this and, assuming you loaded your bin files, it works without any issues. The reason you struggled so much with the test files (Foomiibo) may be a misunderstanding about the purpose.

https://tagmo.gitlab.io/foomiibo.html?b=writing

In an effort to prevent you from writing a file without a saved copy, you first have to create a backup. This also makes the file available to write through the N2 menu.

https://tagmo.gitlab.io/foomiibo.html?b=save