There should be a way to locally set the properties. It is ok to take the default from the settings menu of the document, yet it may well be that in different locations different values must be applied.
I suggest to add an optional argument, which creates an editable annotation at the operator inside the formula. Setting on formula region level would not be sufficient, just think of programs.

Here is an example for approx equal:

Martin KraskaPre-configured portable distribution of SMath Studio: https://en.smath.info/wiki/SMath%20with%20Plugins.ashx