How the VS design surface treats absolute positioning and selection is not something we can control. The design-time mode is quite close to IE5.5 and it has a huge number of peculiarities and odd behaviors.
You can find attached a small video and sample where I reproduce similar behavior with stnadard HTML elements - first, you will see that the cursor is in the body element, then clicking on the red div focuses the script manager (clearly demonstrated near the end when I press F4 and get the Properties window for the script manager).
Using the design-mode in VS for a website is not likely to result in the expected site in an actual browser. This mode is a remnant from the Winforms origins of the webforms platform, but I do not find it reliable.
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