The overrun is a per mailbox flag that is set per message. It is very rarely seen sent unless the traffic is overloading the mailboxes (not necessarily the bus). But because the ISR queues and frees the mailbox as fast as possible it's able to pull the next message in without being overrun. If you decide to do non-interrupt, polling mode, considering loop delays, then you may see the overrun flag appear in a message. Also keep in mind that only the last mailbox will overrun in many mailboxes accept the same frame.
Example, with interrupts off, and not reading the mailboxes, lets say you have 8 reception mailboxes accepting the same frames.
The first 7 would occupy a message but the 8th is a bit different (actually, its always the last one that does). If 8th is also full, and the next message comes in from the SMB (serial message buffer holding next frame to drop into a mailbox, done via hardware), flexcan will see the 8 mailboxes full, however, ONLY the 8th mailbox will be overwritten with the new frame and the overrun flag would be set. The other mailboxes will not be shown as overrun, so when you read their frames they wont be set.