The docs are pretty terrible about recommending how to correct this issue.

The preferred way is to fix change the property names at the data source, so they match the id and text that Select2 is expecting. We understand that this isn't always possible, which is why we have a few hooks where you can do the mapping on the client side.

This is covered briefly in the 4.0.0 announcement:
https://select2.github.io/announcements-4.0.html#changed-id

I'm going to mark this as a documentation issue.

May be create options for this keys?

$.fn.select2.defaults.set("pk-prop", "id");
$.fn.select2.defaults.set("text-prop", "text");

It allows you to work with own format objects wihtout transformation object.