In one of my previous projects we had the following situation: a very big company (single legal entity, so 1 company code) has 6 separate sales organizations and each of them manages credit control separately (so 6 credit control areas).
As you have already observed, we cannot assign all credit control areas to this single company code.
So I left the credit control area in the assignment to company code to be blank and set overwrite credit control area to 'X'.
OB38 gives you just the default credit control area and to be on the safe side, I decided to leave it blank (in case the field is not populated at all, we can get the list of problematic documents in a report, but if the user forgot to change some predefaulted value or if an automatic program did not update this field, I cannot find out which documents are wrong).
In case you post a FI document from FB01 (for example incoming payment), it is very easy to make a mistake - with the described configuration you have to specify the credit control area manually to update the account for the credit control area. Still I would not want to allow posting to credit control areas which do not belong to the sales organizations for this company code. So I set the 6 credit control areas as premitted for this company code.
This is where permitted credit control areas are really useful (because FI does not 'know' about sales area to credit control area assignments when we have postings not originating from SD).