Is Jesus also God the Father and God the Holy Spirit? No. In the context Thomas' declaration of "My Lord and my God!" is only referring to him as God the Son. Likewise, the title of "Mother of God" is only referring to her motherhood of Jesus, God the Son, who is the Son of God and the Son of Mary. Not really hard to understand if you want to.
The primary difference, and it's a huge one, is that Thomas' statement is recorded in the text. And as you note...it is about context.
No where in the NT do we have Mary refereed to as the "Mother of God".
Why? For the reasons I've already stated.
Not really hard to understand if you want to.
And where in the Bible does it say that our faith is to be based solely on the Bible?