If an Apple Authorised Service Provider examines an iPhone and says that the charging connector is burnt or damaged and the logic board needs to be replaced, this generally indicates that the charging connector is not treated as a simple, independently replaceable component in that particular iPhone model.
Unlike the battery, which is a separate component that can be disconnected from the logic board and replaced, the charging connector assembly may be soldered or otherwise integrated into the device's internal circuitry. Depending on the iPhone model, the connector may be mounted directly to the logic board or connected to it through a separate flex/charging assembly. Therefore, the exact construction varies by model.
The important point is that the charging connector is not necessarily a plug-in component that an authorised technician can simply unplug from the logic board and replace in the same manner as a battery. If the connector or the circuitry around it has suffered significant electrical or physical damage, Apple may prescribe replacement of the entire logic-board assembly rather than attempting a board-level repair.
This is also why a statement such as “the charging connector is burnt, so the logic board has to be replaced” does not necessarily mean that the entire board has physically burnt. The damage may be confined to the connector, its solder joints, charging circuitry, or related components on the board. Apple's authorised repair procedure may nevertheless specify replacement of the complete logic board because Apple generally uses approved module-level repair procedures rather than component-level microsoldering.