That's just true for importing a Core Unit file in addition to already selected units on one side. For example you can't buy units for the Axis and THEN you want to import the Core Units (or campaign units as they are called I believe). Then the previous bought units are overwritten.
But you can import an Axis Core Units file and then a Allied Core Unit file and voila you got both Core Units in the editor. I tried it for a campaign I am designing by myself and just tried it again. It works.
Step by step explanation:
Open Scenario Editor
Adjust Mission parameters (date etc.)
Don't load a map you don't need it
Purchase units for one side
Save "Scenario" as for example RussianOOB
Do the same for the other side (with a blank "scenario" without the other sides units and call it GermanOOB
Open a new blank scenario choose parameters and the map you want to play on.
Import campaign units GermanOOB for the Axis (in Unit purchase screen)
Import campaign units RussianOOB for Allied
Now you just have to delete unused parts of the OOB! Also these OOB can easily be edited after the battles. And for a new battle you just load the edited OOBs. You can even add units to the OOB Core Unit later and save it as a new core unit file.
I tested it and it works like a charm but maybe I missed something and I am totally wrong.
For me it is the only way to deal with larger formations over the course of a operation and maintain something like continuity without a brutal workload.
@Ithikial : I uploaded two fake OOBs in the Russian Dropbox folder. Maybe you want to give it a try!