I think that in order to understand the answer, you're going to have to shift from thinking about syntax as word-based to thinking about it as constituent based and hierarchically phrasal. Some Hebrew "words" have more than one syntax label (e.g., when there is a cliticized pronoun) and some words actually share a syntax label (e.g., when they constitute a compound), though in the latter case the trees duplicate the label as a convenience. And one word may have a label (e.g., appositive) but the phrase indicated by the label doesn't end with the word but includes a few more (e.g., when the appositive has its own adjuncts).
The searches don't behave any differently than the trees, as long as one understands the nature of the syntax -- hierarchical and phrasal. This is true whether a phrase consists of one word or forty. And perhaps that's where you should begin by thinking -- in syntax, there is no such thing as a word. There are constituents, which may be simple or complex. They are all phrasal, even if the phrase consists of one item.
The way the syntax was really built was to use the phrases in searching. The non-phrasal options, which use "word" only as a convenience (what other label would users understand as indicating a simple constituent without any modifiers?), are necessary in order to drill down within the phrasal structure to identify the syntactic constituents (smaller phrases) within a larger phrase. Since it is obviously impractical to avoid providing a simple syntax label to insert when looking for constituents that are simple enough that a single morph is co-extensive with a syntactic role, we provided the non-phrasal "word" options.
Unless this has been confusing across-the-board even though few have articulated it as you have here, I would venture to say that this approach can be taken as fairly intuitive. In fact, from working with a variety of users, I suspect that the way it operates appears simpler than even my description here, which is probably going to seem a bit tortured for most.
But if this is not correct and there has been general confusion about the words versus phrases, others need to chime in so we can re-evaluate the searching interface (well, at least the labels of the items in the interface).
Edited by Robert Holmstedt, 01 December 2016 - 08:43 AM.