The behaviour is not currently configurable. We haven’t identified a configuration option that would be understandable and easy enough to use while still solving all instances of this sort of conflict with the website. There are new browser technologies (such as intersection observers) which might allow us to decrease the chance of an overlap occurring without resorting to the addition of additional configuration switches for people to learn.
The problem is very much on my radar and I hope to be able to give some more detailed thought to how to improve the situation later in the year.
Until then, a partial workaround is to use the Keyboard shortcut to display the matches instead; or click on the matched entry in the main Kee popup in your browser toolbar.