There are actually 10 differences (in spelling others invlove large letters. The example you cite is a different letter while the other nine are malei/chaser differences.
Furthermore there are several cases where our sifrei Torah differ from the Gemara’s. The gemara makes derashas lehalacha based on chaseiros we dont have (see sanhedrin daf daled keronos and Totafos)
Within the Hlachic process as long as rules are followed multiple approaches may eb correct. For teimanim following their mesorah, their sifrei Torah are correct for ashkenazim following theirs theirs is correct. And for The Ribono shel olam both are correct.