Yes, the BOINC in-build throttle is frankly numb brained stupid and not in any way designed to provide smooth computing. Rather, it is purely designed as a crude thermal control, mostly for laptops. WCG operates a default of 60% or 3 seconds running, 2 pause, which keeps those lappies reasonably cool.

If temperature is a concern, set BOINC to 100% and use TThrottle (for Windows XP and up), then set the temp ceiling.

When wanting some permanent headroom like I want for lackless response, use ThreadMaster GUI. I've got it set to... 96% on my laptop, which sits on a coolerpad. TMG allows individual science control as not all sciences are equally heavy.

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edit: Maybe knreed/WCG team would consider adding a comment to the Device Profile CPU% field "Use no more than: 60 % of processor time" Note: Only needed for laptops when a temperature concern exists" or something to that effect.

Actually you should notice a speed increase when boinc is at 100% because all cores are "activated and warmed up".
At least I do.

It would be less than 96% because the cores need to start to be used again, there is a small delay before they are running normally again. Also, if the cores drop speed, then this will have to rise. Im not sure how long that takes on you i5, but it can be around 2 sec on other CPUs. If that is happening performance will be well short of 96%
Don't think you are saving on power either, you're not, and in terms of power usage per performance, you lose a right bit there too. Basically stay away from setting CPU % time usage, unless your system is overheating, and can't use better software to deal with it.