The Tibetan alphabet contains two letters whose names are both a, and confusing them makes a syllable unreadable.
A chung, the small a, is the twenty-third letter. A chen, the great a, is the thirtieth and last, and closes the recitation. They are separate characters with separate shapes and separate offices, and they are not variants of each other.
Their jobs barely overlap. A chen is the vowel carrier: where a Tibetan syllable begins with a vowel, a chen supplies the consonant shape that a vowel sign needs to attach to, and with no sign upon it the bare letter is read a. A chung is a weak consonant that works as a prefix, as a suffix, and as a mark of vowel length in Sanskrit transcription, and it is only rarely the root of a syllable at all.
The names encode the distinction and the transliteration preserves it, which is one of the arguments for using a transliteration rather than a phonetic rendering: a system that wrote both as a would destroy information that the script keeps.
The pair matters beyond the alphabet chart because dictionaries file by root letter. A syllable whose small a is a prefix is filed under the letter after it. A syllable whose great a is the root is filed at the end. Getting this wrong sends a reader to the wrong end of the book.