You appear to be mixing the v2 and v3 approaches. The MathJax.Hub.Config() call is part of the v2 API, while MathJax.typesetPromise() is v3. If the latter function is running, then you are using version 3, and the v2 configuration is not being processed at all (it is not that MathJax.typesetPromise() resets it, it was never set in the first place).
See the "Upgrading from v2 to v3" documentation at
for details about the differences in the two versions. There is a configuration conversion tool at
that will help you convert your current v2 configuration to the corresponding v3 one. There are configuration options that correspond to the displayAlign and displayIndent ones that you are using, but they are in the configuration for the specific output renderer you are using (which you don't mention). Use the converter and you should be able to see if v3 will work for you.
Davide