Your savings by merging your changes into a single file are negligible - browsers heavily cache static files like javascript and css, so on a typical session browsing one's site, the css will only be downloaded once (the rest will be just head requests checking to see if the file has changed).

The advantages (well to you, not your end users), far outweigh the bandwidth savings from combining the two files. If you combine the two files, upgrades will require more work (something we're working on reducing), since now you have to go through the css diffs. One case of this being difficult and prone to error would be if we rearranged the contents of the css file (although we'll try not to do such a thing). If you only had your changes in the custom.css, then the change wouldn't affect you - you probably won't even have to worry about looking at the css diffs.

So the difference now is 2 downloads (size of core.css + custom.css) + 2 head requests + no work during upgrades vs 1 download + 1 head request + going through diffs making sure you haven't missed anything every upgrade.

Adrian