You can use the source version to generate the compiled version. The compiled version is fine if you want to use bootstrap unchanged, just override bits with your own stylesheet, but if you want to make bigger changes to it (for example using a different grid system), altering the compiled version is very hard work. If you use the source version, instead of having to make very messy changes to the compiled version, you can make small, simple changes to the LESS files then recompile them to CSS.
There is optimisation to be had as well - if there are bits you don't use, e.g. modals, you can just comment out one line in a LESS file. Similarly you can build a javascript library that only contains teh components you are using.
