The answer is like you said that it is the opinion of the Gr"a. It is quoted from Rabbi Chaim of Volozhin that the Gr"a held any smaller sized Talis Katan to be Hotzaah on Shabbos. Reb Menashe Klein (Mishneh Halakhot) and Rav Moshe Sternbuch in Halichos Hagr"a pg. 38 explain that the opinion is based on the fact that the Torah only required a garment that is of size one will use it to go into a marketplace. Therefore they explain that in the time of the Gr"a they only wore long garments, so only with a long garment one fulfils tzitzis. However, in our time that it is the norm to where short jackets even the Gr"a will hold you fulfil the mitzvah.
Also Rabbi Sternbuch brings that Rav Moshe Feinstein held that it is impossible for the Gr"a to have said such a thing and he held it was the mistake of a scribe and one does not need to be concerned for this opinion.
Obviously the above is an answer to our minhag, however it would appear that the Rabbonim who where these tzitzis do so only as a Chumra.