The Freedom of Information request has an interesting passage - "all records must be certified by the district where the event occurred as a true copy of the register entry, before the General Register Office is able to provide a copy of that event either by certificate or PDF". If the GRO has to contact a district office before sending out a certificate maybe the irregular delays are due to different district offices taking different amounts of time.
No, you've misunderstood the process. It comes up here fairly regularly, and if you do a search for "GRO quarterly returns" (without the quotes) you should find some relevant discussions.
Births, marriages and deaths are registered at a local register office, and once a quarter a copy of these records is sent off to the GRO with a signed certificate to the effect that they are a true copy of the entries in the register held in the office.
Marriages can also take place and be registered at a place of worship, with the minister acting as registrar; in this case the minister writes out the quarterly return and certifies that it is a true copy of the register that he/she holds. The minister sends the quarterly return to the local register office, and they collate the returns for the whole district and send them off to the GRO.
The certification mentioned in the Freedom of Information request has always been part of the process - or to put it another way, if the GRO has a BMD record, it was already certified when the GRO received it.