The CRS tool uses only a subset of your information to guess your score. Which is why sometimes the actual EE score could be more. I added ALL my degrees during EE profile creation and which is why I needed to get all ECAs. However I read later that you can add the degrees later on during additional information. See Education Credentials Assessment (ECA) for all degrees? for other answers. I’m not sure how to do this though, since I went through the pain to get my BE ECA.
The agencies that I got my ECA specifically say that the transcripts should be mailed directly from the university to the agency. If those words are written for the agency you are using, the transcripts have to go directly. Don’t worry, Indian universities will take their own sweet time to do this! Pune University took 2-3 months to mail the transcript with no updates whatsoever.