Seems odd that just clicking does nothing,
Clicking into the intervals pane does do something: it moves the focus there and places the row cursor where you clicked. Being able to click where you want to move the focus, without messing up what's already in thee, is a very big deal. You need to do that constantly, probably more than anything else, so that's why in Windows and in many other contexts a single click does that, moves the focus to where you want.
Suppose you have three windows open: an image, the image's table, and drawing. Clicking into any one of them moves the focus there and the contents pane reacts automatically to the context you've chosen. Clicking into the contents pane's intervals panel allows you to move the focus there, so commands like Ctrl-A to select all rows or Ctrl-I to invert the selection of rows operate on the intervals rows, and not (if the focus were on a thematically formatted drawing), selecting all objects in the drawing or inverting the selection of objects in a drawing.
In another example, clicking the row cursor onto a cell in a table not only moves the focus to that table window, it also moves the focus to that row and column for subsequent moves, like a Ctrl-F for Find being readied to use that particular column by default.
It also makes sense not to have something as powerful as a selection be done with a mouse click action that can easily be a mistake. Click somewhere to move the focus and if you click wrong, it's no big deal. Click again on the right window or panel you desire, with no harm done.
In contrast, suppose you've created an intricate selection in the interval rows panel (could be dozens of rows), or have cleverly selected just the right collection of objects out of many in a drawing: if a simple click changed the selection (and the move to select should be the same move everywhere) to what you clicked on, when you intended to click and drag to just pan the view you could easily click and... good-bye, intricate selection.
I use very many different software packages, with proficiency in a fair number of them, but the speed and efficiency of the mouse moves in Manifold is truly exceptional. I particularly like the ensemble of click-and-drag to pan a display and a zoom box on the right-click-and-drag mouse buttons. Sure wish those were available in other software. Ctrl-click also is a great default mouse move for selection. It's very fast and easy to do and at the same time not something that leads to accidents.
I agree it's something you have to learn. But that's true, as far as I can tell, of all very efficient interfaces for sophisticated products. They're designed to make workflow very efficient for people who have learned them and use them as a working tool. That's a tradeoff as compared to the more limited set normally used for products that don't have much richness or which are intended to be easily picked up and remembered by people who use them rarely. You pay the price for that up-front simplicity with less efficient workflow in regular workflow once you learn the thing.