Science applications running under BOINC run at a low priority anyway, so such a setting would be useless. Especially so since "setting 100%" would then mean you're running at a normal priority. At this moment science applications go out of the way of other programs running at a higher priority.

And if that doesn't work for you, adjust the "Suspend work if CPU usage is above X%" preference in your preferences, which will stop BOINC and its science applications in their threads when the CPU cycles of any other application get to 25% or more.

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...how to set the BOINC client CPU usage to run at one value when using the computer, and another when not used for x minutes? eg. Run at 20% when I'm working, run at 100% when computer not used for 5 mins.

Unfortunately this remains an unfulfilled wish already for years.

[...] this would be an incredibly useful feature!

Indeed :-(

Peter