There are many reasons why breaking this habit is beneficial. Firstly, it is highly unlikely that your finger will actually be in the optimum position for the playing the next note when raking to the string below. This will become more obvious as your tone develops and improves. You are likely to notice differences in tone between the higher string and the string below it that go beyond the characteristics of the strings themselves.
Secondly we do not always want to play everything apoyando (rest stroke). This may be due to the tone we are seeking or because we don't want to mute the strings below etc. Raking, but its very nature, is a rest stroke technique. By forming the habit of alternating where possible, it will be easy to do descending scale runs in both apoyando and tirando down the track.
Lastly, some argue that it is quicker to always alternate. There are, however, others that dispute this argument.
I think the main thing is that you want to be able to consciously choose whether to do an action like raking. At the moment, I think you have admitted that this has become habitual and sub-conscious. For this reason, learning to cross strings while alternating is beneficial and in my opinion is best develop as early as possible. Once you are comfortable doing both, you then have different tools that you can choose to use depending on the passage/situation.