I’m glad I could help!
Even though I’ve been using DEVONthink for over 10 years, I don’t consider myself an expert. But this was an easy question for me to quickly answer.
(A quick note on terminology to help keep communication clear: “the DT tab” is referred to as the Sorter. And it doesn’t have to be shown as a tab on the lower right of the screen – there are various options in the preferences.)
I will echo @chrillek and ask you to consider your choice to index all your files. Why did you choose this? Maybe give the help section on Importing & Indexing a (re)read. Importing is the default for a reason.
From your original post I get the impression you’re a bit uncomfortable with having your files “hidden” in a database. But there is no lock-in and it’s very easy to export. (I think the only exception is custom metadata, but there are options there as well. And this potential problem goes for both indexed and imported items.)