Rationale behind Mozhi scheme
My primary principle behind the scheme is this: The most intuitive scheme for Malayalees. As you can see this principle is different from phonetically accurate scheme. Traditionally our transliteration habits are different from that of North. For example, consider the characters ത, റ്റ & ച.
To simplify the things, Mozhi uses the rule was to append 'h' after the letters for ഖരം and മൃദു to get അതിഖരം and ഘോഷം.
Also, I didn't want to give different sequence for conjunct letters other than their component letters. So, if 'Ta' is ട then 'TTa' should be 'ട്ട'. This simplifies what the user needs to remember.
With these rules in mind, we have following Malayalam letters: ട, ഡ, ത, ദ, റ്റ and just two English letters: d, t to spare (I am not considering അതിഖരം and ഘോഷം now, because they can be produced by the 'h' rule).
Since malayalees are very adamant about 'ത = tha', we cannot use 't' for 'ട', because, then 'th' will become 'ഠ' by the h-rule. So, 't' was given to 'റ്റ' which does not have aspiration.
'ത വര്ഗ്ഗം' letters are more used in the language than the 'ട വര്ഗ്ഗം'. So 'ട വര്ഗ്ഗം' had to be compromised with uppercase letters which was the only available choice left.
If you look at the scheme there is one more symmetry. That is, 'ത വര്ഗ്ഗം' is all small case and 'ട വര്ഗ്ഗം' is just the corresponding uppercase. This also help people to memorize the scheme.