While true, unless I'm mistaken, markers (I assume you're referring to tags) can be nested to provide a pseudo-folder hierarchy, and with proper filters you can remove the "inbox" tag and have the mail only show up under the specific tag.
TBH I don't fully mind it, it lets you classify an email in multiple ways (eg "See Later" as well as "Work related").
Perhaps Outlook is difficult to configure. Thunderbird is intuitive.
Biology is a great example because of just how important digital record management is to experimentation in the field.