Normally yes, they are just for purposes when the CofA or ARC is not valid and needs to be ferried and/or for flight test purposes.
However there was a period a few years ago when some aircraft being built to LSA standards were given what came to be known as 'enduring permits' in lieu of a CofA because an appropriate certification standard for them did not exist in EASA land. These were factory built aircraft and above the microlight weight limit, so in the EASA domain.
I believe they had some restrictions on their permits such as "non-commercial" operations only, but wondered if anyone had an example of the precise wording.