Thanks Peter.
At the moment I have 3 board in my desk: an NXP (Freescale marked actually) dev board and 2 of our custom boards. With one of them I played a bit just to try and disable the BIST and enable it again. Most likely this will never be used but wanted to make sure we can do it. The other board hasn't been modified "BIST wise", so is used for reference.
When disabling BIST, whenever I check the LBIST or MBIST completion register, it's always not finished, which I guess is the sign of BIST not being performed. When the DCF record to activate BIST is set again, I check the completion register for LBIST and MBIST and both report all test as finished, as expected, but as said, results in LBIST are not all OK.
Following is a capture of the Flash on the eval board:

The same capture from our custom board used for reference (no BIST modified):

Last the same capture from our custom board used to test (BIST records have been modified several times):

Please keep in mind none of the boards report all LBIST tests as successful: dev board reports a problem on LBIST0 and the other 2 on LBIST2 and LBIST3. The firmware in all of them is the same.
I'm using S32 Design Studio and for reading the LBIST result I'm using this define found on MPC5744P.h file (automatically added when creating the project), version 6.0.0:
#define STCU_LBS STCU.LBS.R /* STCU2 Startup LBIST Status Register */
Thanks.