The Op seems to be under the impression that 900Mhz ist default and anything below is throttling.
725Mhz is the default clock speed of the 650M with GDDR5.
900 Mhz is the Boost aka Turbo and how much it boosts depends on the workload.
GTA4 apparently simply consumes too much. Also the quality of the DIE plays a part. As it measures outside the chip the real power consumption some that got a cold chip will get better Turbo out of it than those with slightly hotter chips. Much the same as some can overclock higher with out problems than others. Also since according to Anandtech power consumption is measured, better cooling won't change too much about it. Heat has some impact on power consumption but only some.
Read up on Trubo boost.
http://www.anandtech.com/show/5699/nvidia-geforce-gtx-680-review/4
What you are experiencing is not throttling just not as great Turbo speeds.
If you don't want to deal with all this just over clock the chip. Adjusting the power target would really be the way to go. I don't have a 650M notebook but maybe some notebook over clocking tools allow it already like on the Desktop. Otherwise just set some custom fixed over clock as suggested, as long as heat stays reasonable and the power supply + battery can handle it.