I mean, yes and no.

You are assuming that Lithuanian language became formalised when Lithuania was united under one government. Instead, most of language formalisation happened between 1880s and 1920s, when Lithuanian speaking population was actually divided between Prussian and Tzarist Russian empires. While most of the people lived in Tzarist Russia, writing in Lithuanian in Latin script was forbidden there.

Instead, books in Latin script were printed in Prussia and distributed in Russia illegally. A handful of people like J. Basanavičius and V. Kudirka ended up in charge of printing most of those books and it made it easy to set language standards. Achieving such a monopoly with a bigger language would be much more difficult.

That is also why formal Lithuanian is based on one ethnic dialect that was spoken in Prussia.