For Sega CD games, either way will -work-, but that doesn't imply it's perfect copy.
Up until recently I have been pushing for mode1/2048 images made with CDRWin, but I have come to the conclusion CDRWin doesn't bother to copy everything from the disc exactly as it is, so I now hate CDRWin and would like kick the fuckers from Goldenhawk in the nuts for creating a program that acts in such a manner.
Sega CD discs have 150 bad (or unreadable, or something) sectors at the end of the data track, which cause issues with applications trying to extract the data in mode1/2048 format. I've known this for a while, but it never really caused me any concern, because CDRWin would happily make a full mode1/2048 disc image without any sort of resistance.
After a (heated) discussion with someone (sorry derfunk)who told me that Nero would not burn the image of Earthworm Jim I had made in this fashion, I did some testing and realized CDRWin would see these sectors on the disc, be thoroughly confused, and decide they were not worth the trouble, thus moving on without a second thought. The problem is that the TOC of the disc is now not accurate due to the difference in length of the data track in the image compared to the data track on the original disc. This causes problems with Nero and Blindwrite, but CDRWin will burn the image and it seems to work fine in an actual machine.
After some testing, I discovered Blindread (of the Blindwrite suite) and CloneCD will both read all the data from the disc and put it in an image, although both of these programs create only mode1/2352 (raw) images. This is due to the original purpose of these programs, reading everything from a discs whether it was supposed to be an error or not. Just to be complete, I tried making a mode1/2352 image with CDRWin, and it continued to skip the bad sectors.
So to answer the question, I guess, you can rip in either mode1/2048 or mode1/2352 with the program of your choosing, and burn the image with whatever program will accept it, and it will probably work. In my professional opinion (I am hereby declaring myself a professional), it would be best to use Blindread to rip the image to a bin/cue.
PS. I haven't yet burned a Blindread image of a Sega CD game, but I will sometime this week and will report if it works or not.