Where would the checkboxes go in the tab order if we did that? Wouldn't it cause problems for people who want to tab to the checkboxes, since they'd expect them to come after the control they are directly below and related to?
(You can use alt-x to jump straight to Containing Text.)
Yes, I agree, that's good point from the GUI schoolbook, but, in practice, I only jump between those two fields (by tab and shift-tab; I don't ever use other shortcuts) and rarely or never adjust checkboxes.
In my opinion, edit boxes are way too wide, so I would move checkboxes right, in a new column, exactly as you already have date/time/size.
Unfortunately, we have other users to consider as well.
That would not affect the tab order. The checkboxes would still be related to the Name control, and come after it in the UI layout, so they'd come after it in the tab order as well.
It depends what the definition of strangeness is. If you are looking for sort by relevance, it wouldn't be strange at all.
Note that in the upper part you already have mixed tab order meanings/directions. First you have list of folders, then buttons above, then stuff about results and then checkboxes about folders again.
P.S. You could also put Name matching checkboxes above edit box!