I believe the vowel length distinctions you're referring to are totally stress-related. Assamese has penultimate stress, and thus all second-to-last vowels are longer than other vowels. This has nothing to do with the vowel being written one way or another. Shortening that vowel sounds strange to you because it breaks this consistent rule in Assamese for lengthened vowels in certain positions. However, total contextual licensing of length is evidence of a lack of true vowel length distinction in the language, and thus should not be transcribed.