First off, you need to know your needs first.. the amount of programs you need to install, the type of programs and amount of memories required.. You choose that first, cause if you need 8GB of memories, you need to choose the i5/8GB/256GB.
If 4GB RAM is ok for you, how much space does your programs takes? You don't install it outside the SP3 to your external HDD.. programs should stay with your SP3. So if your programs are bigger than 30GB, please don't get the i3/4GB/64GB version... Just go for the i5/4GB/128GB version instead..
i5 may get hot, but there are ways to work around it. (like you can manually throttle it down)
but if you get the i3 and you ran out of space to install your programs, pushing it to microSD is slower, but you still face data space constrain.
Your HDD is great as a home dock desktop mode for the sp3.. but not to install programs in it.. to hold your movies, your huge collections of art and many large stuffs...
Looking at the heat issue, its not too much of a problem if you don't mind slowing it down.. i5 can be cool by not letting it clock up. The throttling issue you hear is the system forcing the i5 to slow down as its getting too hot, so it only gets hot because its running too fast too hot for the system cooling system to handle.. But clocking down a i5 down looses both heat and its speed advantages over the i3.. in fact it almost brings it on par.
So the considering factor isn't i3 or i5 its memories and SSD space..
64GB model fits my needs of what programs I want to run in the SP3 (as a mobile machine) I am not going to pay another $250 just for another 64GB of SSD space. All SP3 has the same screen, pen, battery, kickstand.
But if you need more space, or more memory, 64GB model is not your choice, please don't think of installing your programs in a external HDD or microSD.. those are for your datas...
You know thy self better