This issue feels like a bug to me. If not I am happy to move it. I am using the Window Move and Window Resize features and I find that the behaviors are not consistent across all windows.
My assumed correct behavior is what I experience for a Safari window. Namely all I need to do is place the cursor anywhere over the window, hold down the appropriate keys, move the cursor and voila the window moves or is resized and I have it configured to make the window active.
I have found that for an MS Excel window I must first make the Excel window the active window and then place the cursor over the top "bar" of the window for the resize/move to occur.
I also have found that when I am using Quick View of a PDF that I have similar behavior with one caveat. I do not need to make the Quick View window the active window. Moving the cursor over the window does make it the active window, but it will not resize/move the window unless the cursor is over the bar across the top of the window.
Not sure when this started I have just returned to using BTT. I am using this on an iMac Pro running Big Sur 11.3.1 and BTT 3.553. If you need any additional info please let me know.
Chip