Thanks. You elegantly explain this issue: Tinderbox is not optimised for zettelkasten process nor specifically designed for it. 
Tinderbox’s Cmd+F find stays nicely out of the way, but once invoked the search bar stays in the view unless you click done. This reflects the fact that not all users need to be using the find feature all the time.
Find searches $Text, $Name and a choice of one user attribute: default selection is $Text and $Name but all 3 options can toggle separately; it also has (toggle-able regex and case-sensitive options in easy reach). It isn’t like DEVONthink search, but nor should we expect it to be. DEVONthink is essentially a repository (an ‘everything bucket’ though that terms is not disparaging in this context). So the sorts of searches we do in DEVONthink are in a very different context.
The way to unpick your problem is to not start out from negative comparisons (it’s not like X). What are you trying to search for (in X or in Tinderbox), i.e. what are you expecting to match? Much of Tinderbox’s depth is in the ability to abstract—by thoughtful use—information either implicit or explicit in a note’s title or $Text. Tool’s like The Archive, which mimic the paper card notions (IOW just one piece of $Text) are forced to embrace the limitations of such a format. This is where understanding can break down as constraint-based choices are assumed to be deliberate design choices rather than best choice in limited context. But it’s not a zero-sum consideration which is why comparing very different designs lead to confusion.
Many of us—probably most humans—place a higher value in what we see literally (so the UI). Thus, if the (think we) understand app A and app B looks different it is—at first sight—worse. But that is a superficial, and likely unintended, analysis. Un helpfully, as an app’s UI can thus stand proxy for the process we effect within it, we falsely assume app A is the correct canonical way to work. That is, I suspect, why the new breed of PKM apps tend to use the same plain text+wiki concept+Markdown as any departure from that—it’s too big risk for developers to use any other metaphor. What’s also forgotten is that useful PKM apps pre-ate this supposed canon.ttbx dates from 2002 (informed by/building on ideas/apps from the 1980s) and TheBrain is from the late 1990s. Sometimes we get sucked into the new. Are one window apps better than the old Mac OS, or is this a case of over venerating the constraints of small/single screen working.
Tinderbox is a far deeper, more featured app than a pure zettelkasten tool. But that should not surprise as the latter is doing a narrow (yet powerful) bounded process—and only that. Making Tinderbox look like a zettelkasten app is a fool’s errand, but only because they start form a different place. Using the zettelkasten method in Tinderbox is tractable but only if not doing so by trying to make a file-less plain text app.
Indeed, zetelkasten—stripped of the magic of the name—essentially means taking thoughtful, limited-scope notes, storing ideas/concepts in a single place, and interlinking freely (but with deliberation). There are lots of ways to do that, but our tendency to confuse UI with process can blind us to alternative—even possibly, better—ways to the same end.