that looks more like a modding related problem, but it effects also the vanilla game and if you doesn't fix it yet, it will be huge problem later, so please read befor move the topic at dev/null/.
First of all, XR does not use "defaupt" as the standard-method of a ware, in case it is no method specified in the production modul. The engine uses in that case simply the first production entry of the ware.
That may strategy, but in case someone add his own entry on first pisition (or ES himself change this in the ware.xml), all fabs without a defined method in the universe use that from this moment AND a lot of fabs doesn't have defined a method yet!
So it would be nice to learn your engine that no-method have to use as fallback "default", befor try to use the first entry.
In case the not specify of methods on some fabs was a prupose, maybe to use a sector-effective methode. you should define that solution too now.
That looks not as a huge problem, but i see in the Teladi-DLC you not always add the default production in ware.xml on first position, so i suppose some of the new DLC-fabs have also not add the fieldsofop - in case you will later change this behavor you will have a lot more patchwork to do.

So please fix this as soon as possible, otherwise now working processes could look like sloppy work later.
The other thing is, we can not add our own methods for produktion yet, because of it looks like the engine ignore them on the produktion modul at the moment.

So we have to use omicron/fieldsofop/alien/malstrom dependent of what is free for the moment - thats possible, but not a good solution at all
So what i ask for:
- define on not specified productions first the try to use the "default" method and then to use the first production-entry of the ware (like it is now)
- fix our dlc fabs in case they will produce with the wrong method
- add the possibility to use our own methods - or discribe us how to add