It is easy to be confused as some airlines refer to excess baggage as ‘cargo’. This is just to differentiate between in-hold and in-cabin travel and not true cargo where your pet can travel independently.

Not all airlines will allow for checked luggage / in-cabin, only cargo (ex. Emirates).
Cargo and commercial are two separate business entities within an airline, not all will do both. There are specific cargo airlines for example.
There are specific holding areas for cargo (temperature controlled etc.) for specific types of cargo goods.
Live animals are referred to as AVI in cargo terms.
IATA has put in place strict regulations and rules regarding the handling of AVI, they are referred to as LAR (Live Animal Regulations)
There are some countries who will only allow pets to enter the country as Cargo, including the UK, Australia, NZ, South Africa, Finland, Dubai…)

Oftentimes the pets going as Cargo are flying with a commercial aircraft, which means that animals travelling as checked luggage and cargo can be in the same compartment in the same aircraft.

HOWEVER, the ground handling from arrival, check-in and loading, including un-loading and handling at arrival are very different and by different teams.

Cargo teams will have specific training, or even be animal professionals, and luggage will be handled by the luggage teams.

What’s inside the LAR?

The LAR covers animal transport of all kinds and contains comprehensive information about the requirements for protected and endangered species, lab animals, livestock and domestic animals.

Applicability (shipper and carrier responsibilities, training, combating illegal trade)
Government regulations (general and variations by country)
Carrier regulations (general, variations by carrier, airline contact information and AVI services)
Reservations and advance arrangements (schedules, routing, interline advance, delivery, accompanying persons)
Animal behaviour (general, disturbance, segregation, sedation, euthanasia, in-flight environment)
Listing, description and species size (taxonomy, alphabetical list, description and size)
Documentation (shipper’s certification, waybill, captain notification, CITES documents, other documents, live animal acceptance checklist)
Container requirements (general, stocking density, marking, labelling)
Handling (animal acceptance, ground handling, loading, feeding and watering, captain’s advice, health and hygiene, OIE recommendations)
CITES (general, documentation, list of states, management authorities by country, Article XI, combatting illegal trade)
Life science logistics for lab animals (health status, animal type and number, species, and container considerations)