Yes, it's true, once upon a time in ancient times Torah Scrolls were brought into synagogues, and were not there initially. This is due to several reasons. Many early synagogues arose in exile, located in ordinary residential buildings. People simply gathered to study or read the Torah in public.
Aron HaKodesh is a relatively new phenomenon. They appeared about 2000 years ago, approximately. And the fact that it was presented in different ways everywhere. In some communities, Aron HaKodesh was a box on wheels that was "imported" into the synagogue or traveled with it.
For the synagogue, the most important thing is first of all the Bimah. It is much older, this element of the synagogue was introduced by Ezra Soifer during the Babylonian Captivity.
The reason for the changes associated with the appearance of Aron HaKodesh in the synagogue is the emergence of Minhagim in Galut conditions. Communities, for the most part, are free to choose the type and structure of their synagogues on their own.
Once upon a time, the location of Aron HaKodesh was not important at all, he could be anywhere. And nowadays its location and direction serve us as the direction of prayer: towards Eretz Israel, towards Jerusalem, towards Kodesh Hakodashim.
Times are passing, new customs are emerging, traditions are being formed, this is normal. A lot has changed in Galut over 2000 years. This is changing even nowadays...