The following is an extract from the Irish Customs Manual on Import VAT:

Control of Movement – There is no specific customs function in controlling the movement of the
goods to the other Member State. Such movement is governed by the arrangements which apply
to intra-Community transactions. However, any case where concern arises that the requirements
to forward the goods to the other Member State are not being met should be reported to the
Revenue District responsible for the importer’s tax affairs for appropriate follow up enquiries.

Since procedure 42 is defined as “release for free circulation….,” I agree that these are Union goods.  Customs officials in a member state through which the goods are being moved have no function that I am aware of.  I am not sure what the “submitted documents” mentioned can be.  Presumably the submission of documents to Bulgarian Customs is the cause of the checks carried out.

Since procedure 42 derives from Directive 2006/112/EC its correct operation is a matter for the VAT authorities after import clearance is given by the Customs Office of Import.